Dear jewettaij：
We can open “oplsaa.lt” file in moltemplate/force_fields.In line 8217,it is "@improper:055_055_X_055 @atom:_b_a*_d*_i55 @atom:_b_a*_d*_i55 @atom:* @atom:_b_a*_d*_i55". I think we should use “i055” rather than “i55” in the second half of the sentence .I don’t know if my judgment is correct, but I hope this helps to ensure the correctness of the force field file.
Best wishes.
ALEX

I seem to have a pypi specific bug which occasionally occurs when people install using "pip install moltemplate" (ie using pypi to download moltemplate instead of github).

If you installed it that way, then ".lt" files that contain force fields, and some random stuff like popular water molecules were not getting copied to the correct place. That means if you use any of these force fields or water molecules in your simulations, moltemplate will complain that it can't find the .lt file for that force field. (eg "oplsaa.lt").

If you run into this problem, there are two easy work-arounds:

1. Just download the file you need from: https://github.com/jewettaij/moltemplate/tree/master/moltemplate/force_fields/
   ...and then move it to the directory where you are running moltemplate, and try again.

2. Alternatively, try downloading moltemplate from git instead (bypassing pypi), and install it by changing to the "moltemplate" directory and entering:
   pip install .
   (instead of "pip install moltemplate")
   This problem only occurred when python 3, not python 2.7, in conjunction with pypi. And, again, this problem never occurred when downloading moltemplate directly from git (or from the moltemplate.org web page, regardless of whether you were using python 3 or 2.7).

Details

I must be screwing up the format of the "package_data" entry in the "setup.py" file,

package_data={'moltemplate': ['force_fields/*.lt']}

...because the various .LT files which are stored (in the "force_fields" directory) there are not getting copied to where they need to go. But this only occurs when downloading from pypi ("pip install moltemplate") using python 3 or later. If anyone has any suggestions, please issue a pull request (or send me an email if that's easier)
http://moltemplate.org/images/author_email.png

This is line 226 of the script:
if ! "${PY_SCR_DIR}/scripts/moltemplate.sh" "${BASE_NAME}.lt" \

The correct line should have been:
if ! "${PY_SCR_DIR}/moltemplate.sh" "${BASE_NAME}.lt" \

Dear Andrew,

How do I convert this Ethylene glycol topology and parameter set in GROMACS format to LAMMPS format?

So, I have this OPLS-AA file and the ethlyene glycol molecule file from ATB.

The set was obtained from this paper https://doi.org/10.1021/jp109914s

#define _FF_OPLS
#define _FF_OPLSAA

[ defaults ]
; nbfunc    comb-rule   gen-pairs   fudgeLJ fudgeQQ
       1            3         yes       0.5     0.5

[ atomtypes ]
; name  bond_type      mass    charge   ptype          sigma      epsilon
    CG      CG  6  12.01100    0.1650       A    3.50000e-01  2.76144e-01
    HG      HG  1   1.00800    0.0600       A    2.50000e-01  1.25520e-01
    OG      OG  8  15.99940   -0.7200       A    3.00000e-01  7.11280e-01
    HO      HO  1   1.00800    0.4350       A    0.00000e+00  0.00000e+00

[ bondtypes ]
;  i     j   func         b0         kb
  CG    CG      1    0.15290   224262.0
  CG    HG      1    0.10900   284512.0
  CG    OG      1    0.14300   267776.0
  OG    HO      1    0.09450   462750.4

[ angletypes ]
;  i     j     k   func      th0      cth
  CG    CG    OG      1   108.00   418.40
  CG    CG    HG      1   110.70   313.80
  HG    CG    HG      1   107.80   276.14
  HG    CG    OG      1   109.50   292.88
  CG    OG    HO      1   108.50   460.24

[ dihedraltypes ]
;   i    j     k     l   func  coefficients
   OG    CG    CG    OG  3    9.852  11.989   4.987 -26.828   0.000   0.000
   CG    CG    OG    HO  3   -0.141   5.591   3.156  -8.606   0.000   0.000

; Fourier coefficients
; angle    F1      F2      F3
; OCCO   16.264  -4.987  13.414
; CCOH    1.727  -3.156   4.303

Thank you for your time and support.

Best regards,
Yunes Salman

Dear Andrew Jewett,

I tried to run the example Coarse-grained lipid bilayer using the MARTINI force field and PACKMOL. When I run " moltemplate.sh -xyz system.xyz system.lt" comment there was an error like this.

Error: Number of atoms in coordinate file provided by user (9600)
does not match the number of atoms generated in ttree file (9216)

Could you please show me how to fix this error.
Ps: I didn't change any thing in your input files

Thank you in advance for your help.

Best regards

Hi Andrew. I've been looking at scripts (sh) but I'm not very good with this programming language, I didn't understand it very well. I'm in doubt about the bonds_type property of the GPSettings class, in genpoly. I know that genpoly_lt does not check the bond and atom type, but moltemplate.sh does. I'm trying to use types present in force field, like "084_084" from oplsaa, but moltemplate says the type doesn't have the necessary parameters. Where can I learn more about the valid types of bonds_type and bonds_atoms?

When being built, self.l_data_pair_coeffs and self.l_data_pairij_coeffs (I'm not sure if others do this too) are identified by a name given by using self.atomtypes_int2name on their atom types
e.g. line 1996 i_str = '@atom:' + self.atomtypes_int2name[i]

However later in the postprocess3 function when checking whether to delete a line or not the, name is converted by the Intify function (line 2992:3005)

atomtype = Intify(split_colon[1])
            if ((not (atomtype in self.needed_atomtypes)) and
                (not ((len(self.atomtype_selection) > 0) and
                      BelongsToSel(atomtype, self.atomtype_selection)))):
                del self.l_data_pair_coeffs[i_line]

and the Intify function fails to recognise the names of the atoms if they were read from comments, causing all pair_coeffs lines to be deleted.

Suggestion:

Replace the Intify functions in these sections with the self.atomtypes_name2int. Since the names are built originally by self.atomtypes_int2name this simply reverts them back to ints.
Example for self.l_data_pair_coeffs (line 2992:3005):

atomtype = self.atomtypes_name2int[split_colon[1]]
            if ((not (atomtype in self.needed_atomtypes)) and
                (not ((len(self.atomtype_selection) > 0) and
                      BelongsToSel(atomtype, self.atomtype_selection)))):
                del self.l_data_pair_coeffs[i_line]

Hello,

The FreeBSD port runs this script as a testsuite:

        @cd ${WRKSRC} && \
                ([ -e shunit2 ] || (${MKDIR} tests/shunit2 && ${RM} tests/shunit2/shunit2 && ${LN} -s ${LOCALBASE}/bin/shunit2 tests/shunit2/shunit2)) && \
                ${SETENV} ${TEST_ENV} bash tests/test_read_coords_pdb.sh && \
                ${SETENV} ${TEST_ENV} bash tests/test_ltemplify.sh && \
                ${SETENV} ${TEST_ENV} bash tests/test_oplsaa.sh && \
                ${SETENV} ${TEST_ENV} bash tests/test_compass.sh && \
                ${SETENV} ${TEST_ENV} python3 tests/test_genpoly_lt.py

In version 2.20.17 it fails like this in the middle:

/disk-samsung/freebsd-ports/science/py-moltemplate/work-py39/stage/usr/local/bin/cleanup_moltemplate.sh: line 227: /disk-samsung/freebsd-ports/science/py-moltemplate/work-py39/stage/usr/local/bin/scripts/moltemplate.sh: No such file or directory
ERROR: cleanup_moltemplate.sh: unable to convert the simplified LT file to LAMMPS files
ASSERT:cleanup_moltemplate.sh failed: system.data missing impropers

Ran 1 test.

FAILED (failures=2)

Hello！
Recently, I am building a polymer interface model. The polymer uses polyvinyl alcohol . The interface plans to use graphene sheet or hexagonal boron nitride sheet . Later, I will consider grafting other polymers on the interface. It is not difficult to build a polymer model using moltemplate,but it seems difficult to build a graphene sheet or hexagonal boron nitride sheet and polymer interface model.
I checked the establishment of the graphene sheet in the example, and I found that the atom types were set by ourselves, such as “@atom:C"，rather than gotten from oplsaa force field. The force field parameters of the polymer interface model can be divided into three parts, the polymer itself;graphene or hexagonal boron nitride;between the polymer and the interface.The first one can be obtained by moltemplate, the second is also simple , such as AIREBO or Tersoff.But the third one seems difficult, because I did not find the appropriate C, B, and N atomic types in oplsaa to build graphene and hexagonal boron nitride sheet, So it is hard for me to get correct pair_coeff parameters between polymer and boron nitride sheets or graphene sheets .
I want to know whether it is possible to bulild a graphene or hexagonal boron nitride sheet in the oplsaa force field through molteplate, and obtain a reasonable pair_coeff parameter between the polymer and the interface?
Thank you!

Hi Andrew.

I'm trying to build a LAMMPS data file through Moltemplate. My system is formed by a carboxylic acid adduct solvated by water. For that, I'm using spce_oplsaa.lt and oplsaa.lt for water and adduct, respectively. I solved several of my issues by means your excellent answers in the LAMMPS forum. However, I have one methodological issues that I can't solve. In particular, it seems to me that Moltemplate generates wrong masses in LAMMPS data file using OPLSAA force field. All masses are being copied from oplsaa.lt to LAMMPS data file. I though that it was a problem in my LT files, but I found the same error using the system.it available example waterSPCE+methane. Do I need to do anything else with oplsaa.lt?

Thanks in advance.
Sincerely,
Raphael

Dear Professor,

I want to use moltemplate to add information such as key corners from the pdb file created by packmol, but when I run:
moltemplate.sh -pdb start.pdb -atomstyle "full" system
lt it reports an error stating:
Error: Number of atoms in coordinate file provided by user (23238) does not match the number of atoms generated in ttree file (9798).

My system is graphene electrode with ionic liquid system,When I was troubleshooting the error, I found that when I read just the graphene or water or Li ions individually, I could read their pdb file coordinates, but when I read them together I had a problem with not being able to match the pdb coordinates.

This problem has been bothering me for a long time, and my lt files are written strictly according to the syntax.Here, I sincerely ask for your help!

Thanks a lot!

Here, I attach my lt files.
case.zip

The dump2data.py utility seems to fail when reading trajectories from simulations that were not run at constant volume (such as NPT simulations). I noticed this when interrupting a constant-pressure simulation and using the dump2data.py program to convert the last frame from the incomplete trajectory to start a new simulation.

I don't need this feature in my own work, so it might be a little while before I get around to fixing this problem.

-Andrew

setup.py says that pytest is required for tests, but it fails to run them:

==================================================================================== test session starts ====================================================================================
platform freebsd13 -- Python 3.8.12, pytest-4.6.11, py-1.9.0, pluggy-0.13.1
rootdir: /disk-samsung/freebsd-ports/science/py-moltemplate/work-py38/moltemplate-2.20.1
plugins: forked-1.0.2, hypothesis-6.32.1, cov-2.9.0, xdist-1.32.0, rerunfailures-10.1, timeout-1.4.2, mock-1.10.4
collected 0 items                                                                                                                                                                           

=============================================================================== no tests ran in 0.09 seconds ================================================================================
*** Error code 5

Version: 2.20.1
Python-3.8
pytest-4.6.11
FreeBSD 13

I'm new to moltemplate, i just installed it and tried to run the carbon nanotube capillary example,
when i try to run the 'moltemplate.sh system.lt'
it shows this error
Error(ttree.StaticObj.Parse()):
Duplicate class/array "unitcells"
This occurs near:
"graphene_walls.lt", line 14
and also near:
"nanotube.lt", line 14
Could you help please?

Hello!

I've been playing around with the dry martini model incldued with moltemplate - I had an error that certain atom masses and atom types were undefined. It seems like this issue cropped up especially surrounding the small bead naming schemes. In particular, throughout the lt file there were references to SP4_bSP4_aSP4_dSP4_iSP4, but the replace command read replace{ @atom:SP4 @atom:SP4_SP4_aP4_dP4_iP4} missing S's before the P's in the longer name causing moltemplate to think there weren't masses defined for these atoms.

There was also one bond coeff not defined - P1-C1, I wasn't sure whether that should be defined or not - I added a coeff for it and marked the location (line 828). The coeff I chose was 1.49375 4.8 (which I think is correct).

I've gone through and corrected (I think) all of these issues - I don't make any promises that anything else in the file is correct. (I marked things I changed with comments). Moltemplate runs with dry martini now at least with these changes.

I've attached the new lt file to this issue report (I had to swap the extension to get github to accept it). Let me know if you have any questions, I hope this helps!

Best,
Zeke

drymartini.txt

In moltemplate.sh:

if which python > /dev/null; then
    PYTHON_COMMAND='python2'
elif which python3 > /dev/null; then
    PYTHON_COMMAND='python3'
else
    echo "Error:  $G_PROGRAM_NAME requires python or python3" >&2
    exit 1
fi

This fails when conda is activated and 'python' leads to python 3+.
If I knew bash well enough I would fix this to check the version with 'python -v'

Hello！
I created a chain of polyvinyl alcohol for all-atoms MD simulation. I choosed the atom 96 and 97 as oxygen and hydrogen atoms of hydroxyl in OPLSAA.
Their charges are -0.683 and 0.418.This is not electrically neutral .Is this because I chose the wrong atom type? Or I need to use another tool to calculate atomic charges？

Thank you！

Dear Moltemplate users,

I have an issue about " There are no atoms in the system".

I build a force-field of PDMS. The force field include atoms I need inside. (The partial code is shown below:)
PForceField {
write_once("In Init") {
units real
atom_style full
bond_style class2
angle_style quartic
dihedral_style opls
pair_style buck
}
#There are 4 atom types: "C" "H" "Si" "O"
write_once("Data Masses") {
@atom:Si 28.085
@atom:C 12.01
@atom:H 1.007
@atom:O 15.999

And I import the force field to my monomer.lt script. (as shown below:)

_import "PForcefield.lt" # contains force-field parameters

monomer inherits PForceField {

write("Data Atoms") {
#atomId molId atomType charge x y z
$atom:Si $mol:... @atom:Si 0.0 -0.637886 0.553288 -0.183695
$atom:O $mol:... @atom:O 0.0 0.248119 -0.271508 -1.283296
$atom:C1 $mol:... @atom:C 0.0 -0.600714 2.369272 -0.648393
$atom:H1 $mol:... @atom:H 0.0 0.439526 2.758433 -0.590174
$atom:H2 $mol:... @atom:H 0.0 -0.977302 2.505258 -1.68573
$atom:H3 $mol:... @atom:H 0.0 -1.241965 2.958313 0.0432318461
$atom:C2 $mol:... @atom:C 0.0 -2.392134 -0.107249 -0.223331
$atom:H4 $mol:... @atom:H 0.0 -2.823555 0.014571 -1.241173
$atom:H5 $mol:... @atom:H 0.0 -2.40159 -1.186807 0.0434449812
$atom:H6 $mol:... @atom:H 0.0 -3.0274 0.446758 0.502263
}
write("Data Bonds") {
#bond-id bond-type atom-id1 atom-id2
$bond:CH31 @bond:Sidechain1 $atom:C1 $atom:H1
$bond:CH32 @bond:Sidechain1 $atom:C1 $atom:H2
$bond:CH33 @bond:Sidechain1 $atom:C1 $atom:H3
$bond:CH34 @bond:Sidechain1 $atom:C2 $atom:H4
$bond:CH35 @bond:Sidechain1 $atom:C2 $atom:H5
$bond:CH36 @bond:Sidechain1 $atom:C2 $atom:H6
$bond:SiC1 @bond:Sidechain2 $atom:Si $atom:C1
$bond:SiC2 @bond:Sidechain2 $atom:Si $atom:C2
$bond:SiO @bond:Backbone $atom:Si $atom:O
}
}_

However, the Error shows:
_Error: There are no atoms in your system. Suggestions:

   Your files must contain at least one
       write("Data Atoms")
   command.  These commands are typically located somewhere in
   one of the molecule object(s) you have defined._

I also try using "new" in my monomer.lt script:

_import "PForcefield.lt" # contains force-field parameters

mon1 = new Si
mon2 = new C
mon3 = new O
mon4 = new H
monomer inherits PForceField {_

It shows:
Error(ttree.PtknsToNode()):
Class or variable "Si" not found
in this context: ".../Si"

Did I do something wrong with creating atoms?

Thank you so much for help and any suggestions in advance

monomer.txt
PForcefield.txt
.

After I installed moltemplate in Ubuntu18.04 (python3) and try to run an example from http://moltemplate.org/visual_examples.html, I got the error as title said. How could I solve it? Thank you!

Thanks for such a great library.

Since pip allows direct installation from remote git repository by running following command,

user@host:~$ pip install git+https://github.com/jewettaij/moltemplate.git

it will be very helpful for new users to add this in README.md, especially who's not familiar with python.

moltemplate_2020-4-04/examples/all_atom/force_field_OPLSAA/
ethylene+benzene
ethylene+benzene_PACKMOL/

For the above examples, the system.data gives 906 atom types as in the following.
I wonder why there are 906 atom types, as the actual atom types in the Atoms section
are few. Just the same as in oplsaa.tt ? Thank you very much.

LAMMPS Description

 2592  atoms
 2376  bonds
 3240  angles
 3456  dihedrals
 3240  impropers

 906  atom types
 379  bond types
 1017  angle types
 800  dihedral types
 6  improper types

Hi, I got the following error message while running ltemplify.py on a system with improper dihedrals:

File "ltemplify.py", line 3901, in PostProcess3
    for improperid in needed_improperids:
NameError: name 'needed_improperids' is not defined

Presumably a self.needed_improperids is needed on line 3901?

Hello！
I found a small problem.I successfully installed moltemplate on my computer which is windows 10 a few days ago.After that,I run a example on it .Its name is "alkane_chain_single" and the file path is “examples\all_atom\force_field_OPLSAA\alkane_chain_single”.

I got the system.data after running the moltemplate. Then I used the VMD to open this file. There was no problem in molecular configuration with VMD. But I found the mass information of all atoms that own to the force field in the system.data . It seems that this wouldn't affect the consequence of simulation.

I think it will be better if the data file just contains the mass information of the atoms of given system. Unfortunately I haven't learned python and how to use python yet. So I don't know how to deal with this small problem.I will start to to learn python and try to address this issue after I finish my current course.And when I'm done, I'll come back and give an answer.

Thank you!

ALEXysd.

Here is a message posted on the LAMMPS mailing list from Daoud El Kadiri.
I am posting it here because I was unable to reproduce the problem on my end, and I am hoping that Daoud or someone else can follow up.:

"I changed my ubuntu from 18.04 to 20.04, and downloaded the last version of moltemplate (before i was using 2020-12-02) and since then i have a problem running moltemplate

When i try to generate lammps input files through "moltemplate.sh -xyz system.xyz -vmd system.lt", the data file generated has all molecules placed on the same coordinates (which is not the case on the .xyz file).

I tried with the files already available in the moltemplate example directory (for example ethylene+benzene_PACKMOL) to be sure the problem wasn't in my own lt files and it still the same

I attached the .xyz file and the data file generated when i run the example "ethylene+benzene_PACKMOL" from the moltemplate examples

Thanks in advance for your help"

        if len(self.l_data_improper_coeffs) > 0:
            l_data_improper_coeffs.insert(
                0, (' ' * self.cindent) + 'write_once(\"' + data_improper_coeffs + '\") {')

should be

        if len(self.l_data_improper_coeffs) > 0:
            self.l_data_improper_coeffs.insert(
                0, (' ' * self.cindent) + 'write_once(\"' + data_improper_coeffs + '\") {')

Hi Andrew,

Attached are the chemical.lt for a simple ethene molecule and the corresponding system.lt. When I followed the guideline and used path/moltemplate.sh system.lt, I found 4 dihedrals in system.data, which doesn't seem make sense as all the atoms in ethene lie in one plane. Please let me know what you think about this. Thanks!

chemical.lt

import "oplsaa.lt"

chemical inherits OPLSAA {
    write('Data Atoms') {
        $atom:0 $mol @atom:88 -0.39937 0.666  -0.000   0.000
        $atom:1 $mol @atom:88 -0.39937 -0.666   0.000  -0.000
        $atom:2 $mol @atom:89 0.199685 1.241  -0.924  -0.000
        $atom:3 $mol @atom:89 0.199685 1.240   0.924  -0.000
        $atom:4 $mol @atom:89 0.199685 -1.240  -0.924   0.000
        $atom:5 $mol @atom:89 0.199685 -1.241   0.925   0.000
    }

    write('Data Bond List') {
        $bond:0 $atom:0 $atom:1
        $bond:1 $atom:0 $atom:2
        $bond:2 $atom:0 $atom:3
        $bond:3 $atom:1 $atom:4
        $bond:4 $atom:1 $atom:5
    }
}

system.lt

import "chemical.lt"

# Periodic boundary conditions
write_once("Data Boundary") {
    0.0  32.0  xlo xhi
    0.0  32.0  ylo yhi
    0.0  64.0  zlo zhi
}

Chemical = new chemical
Chemical.move(0.0, 0.0, 0.0)

system.data

LAMMPS Description

     6  atoms
     5  bonds
     6  angles
     4  dihedrals
     6  impropers

     906  atom types
     379  bond types
     1017  angle types
     800  dihedral types
     6  improper types

  0.0 32.0 xlo xhi
  0.0 32.0 ylo yhi
  0.0 64.0 zlo zhi
...

In the example file for the Mixture of two organic molecules using the OPLSAA force field (Benzene + Ethylene), the above error is coming after running the command: lmp_serial -i run.in.npt

Hello!

I got this error while running moltemplate. I saw that there was a similar issue before but the bug was fixed in v2.20.1. I'm using the current git version so I'm not sure if the bug is in this version again or there's something wrong with my files/input. I'm attaching my files incase you want to reproduce the error.

Hi Andrew.

I was trying to modified a .lt file generated by ATB to fit OPLSAA force field. However, an error occurred as below:

lttree_postprocess.py v0.6.1 2020-10-15

Error(lttree_postprocess.py): near "D7JH_allatom_optimized_geometry.lt", line 272

      Reference to undefined $angle:

            $/angle:bcb/a2     (<--full name)

      (If that angle belongs to a molecule (or other subunit), make sure that
       you specified the correct path which leads to it (using / and ..))

I don't think this error result from mistakes in the .lt file because the assignment for that angle can be found in "ttree_assignments.txt" file.
$/angle:bcb/a2 2 #"D7JH_allatom_optimized_geometry.lt", line 272

This error was omitted when running the script with "-nocheck" flag. However, there will be extra sections of "Angle List", "Dihedral List" and "Improper List" in the .data file.

Could you tell me what's the problem?
Thanks

OK, after about a whole day i finally figure out how to use TIP4P model by using moltemplate and oplsaa.lt
There is a bug to cleanmoltemplate.sh.

After I generate simulation system by moltemplate.sh, it all works well. But after using cleanmoltemplate.sh, those irrelevant information is removed, but add set type charge to system.in.settings. That means we use set charge two times: one in system.in.settings, after pair_coeff etc; another is system.in.charges.

If i want to use TIP4P model, i should not explicitly add a dummy atom M to water.lt, but just assign the charge of M to O, thus LAMMPS would implicitly introduce the dummy atom M to system just if your H2O has the right order. (It is a little bit imcompatible for moltemplate to LAMMPS.) Here is point. I forget that there is a system.in.charges file exists and i just rectify .settings, so .charges override my previous charge assign, so my system always blow up due to no attraction.

Anyway, I think you should do remove the function that cleanmoltemplate.sh copy set charge command to .settings. Or due to simplicity, totally remove the system.in.charges and write set charge to .settings file. Because the meaning of .settings is that settings the parameters of system.

I would pull request a example of how to build TIP4P water system and write a tutorial about how to use oplsaa force field(I think after one week study and try and try and try i can say i understand it). But today it is too late...

Dear developer,

I am using the OPLS-AA parameters from the file oplsaa.lt. May I ask for the improper dihedral X_X_003_004, which one should be the center atom?

Best regards,
Huang Ziru

Hi andrew,

I have a martini based coursegrain simulation in which the size of the box is large. There are 3 species of atoms totaling around 12million atoms. Moltemplate always crashes through the run and it takes forever, is it possible it on multiple cores with mpi/mpiexec.

Hassan

Hi,

I am new to moltemplate, so I am sorry if I asking a (trivial) question here. I wanna create forcefield.lt. Can I use LAMMPS variable command in my script? I would like then use this forcefield.lt as a template and produce a collection of LAMMPS input files by bash scripts.

For instance I want to have the following command in my LAMMPS script

variable cutoff11 equal ${sig1}*1.12246205

where sig1 is then given to LAMMPS as an argument with the command-line option lmp_serial -var sig1 VALUE.

Please see the part of the input file that I want to use variable command in.

example.txt

Thanks

Amir

When GenPoly ParseArgs is used referencing the "-sequence" file, name_sequence_multi is not initialized. This is probably due to the fact that ReadSequence is only executed in main() which is not used in API mode. I think it's something simple to fix, but I believe you have a proposal for a better solution.

Hi,

I am using an Bash environment to run moltemplate on my windows 10 machine. After getting it to recognise moltemplate (v 2.19.12) as an command and making sure it recognises my python installation (v 3.9), I end up with an error message: ValueError: Attempted relative import in non-package, it enters the exception after which Bash presents me with: ImportError: cannot import name OrderedDict.

This happens both on v2.19.12 and v2.19.11 of moltemplate. The ValueError was solved by removing the "." in the moltemplate script. I struggle to find a solution for the import error.

If I write "lttree_check.py" in bash, I get the exact same error message.

I understand that this isn't a bug as per say, but I was hoping I could receive some help in getting it to work.

Thanks for your time!
H2O2

Dear Andrew

When I generated the system. data file for the newest version, I got the error " The number of columns in your data file does not match the LAMMPS atom_style you selected. Use the -atomstyle <style> command line argument." However, if I used the version from July 26, 2020, there is no error. Besides, I tested the example files in the old and the newest version, there is also no error. I tried to space between the columns or arrange columns in align but I cannot pass the error. Can you check it? Thank you very much.
Tue Le

Dear All,

This issue was raised a few months ago but it is closed now and I can't really figure out the solution.

So, I installed moltemplate using
sudo pip3.8 install .
command. I got this message in response:

WARNING: The directory '/home/dawid/.cache/pip' or its parent directory is not owned or is not writable by the current user. The cache has been disabled. Check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag.
Processing /home/dawid/qsar/moltemplate/moltemplate
Requirement already satisfied: numpy in /usr/local/lib/python3.8/dist-packages (from moltemplate==2.19.4) (1.19.3)
Building wheels for collected packages: moltemplate
  Building wheel for moltemplate (setup.py) ... done
  Created wheel for moltemplate: filename=moltemplate-2.19.4-py3-none-any.whl size=947603 sha256=636b2825e6147f767754caf7f16cb1cf018a0eb5cadc160428c2ab31546e2073
  Stored in directory: /tmp/pip-ephem-wheel-cache-12keh4te/wheels/49/fb/77/543625cb3ecfa30c8a7d9be81a554a2159052b2ef9bffcf78e
Successfully built moltemplate
Installing collected packages: moltemplate
Successfully installed moltemplate-2.19.4

So apart from the WARNING, everything seems fine. However, if I run
moltemplate.sh system.lt
I keep on getting this message

  File "/usr/local/bin/lttree_check.py", line 5, in <module>
    from moltemplate.lttree_check import main
ImportError: No module named moltemplate.lttree_check

I can find the lttree_check.py script in my /usr/local/bin directory but there is no moltemplate module.
However in the directory where moltemplate was downloaded I found the moltemlpate.sh script:
/home/dawid/qsar/moltemplate/moltemplate/moltemplate/scripts/moltemplate.sh
When I run it, it seems to work. So I just want to let you know that the reason behind this error is that
moltemplate.sh does not know about the directory where it should look for the *.py modules.

I can't seem to run the menger_cubes example:

moltemplate.sh v2.0.2 2016-12-04

lttree_check.py v0.76 2014-12-19

    "Data Atoms" column format:
    atom-ID molecule-ID atom-type q x y z

lttree_check.py:    parsing the class definitions...
Error(ttree.StaticObj.Parse()):
       Syntax error at or before "menger_cubes.lt", line 48:
       "cells_xz= new".

I looked at the syntax in menger_cubes.lt but can't seem to spot the error. Could you assist please?

After installing my branch of moltemplate with pip, and trying to
run this example

examples/force_field_OPLSAA/alkane_chain_single/moltemplate_files

(The example works when moltemplate is not installed through pip.)

nbody_by_type.pyc v0.18 2014-12-19 (python version < 3)
Error: Unable to locate file "opls_imp"
(Did you mispell the file name?
Check the "nbody_alternate_symmetry/" directory.)

The file it is looking for is
moltemplate/nbody_alternate_symmetry/opls_imp.py

I have been getting this error message.

Traceback (most recent call last):
  File "genpoly_lt.py", line 1084, in <module>
    main()
  File "genpoly_lt.py", line 1071, in main
    genpoly.WriteLTFile(outfile)
  File "genpoly_lt.py", line 663, in WriteLTFile
    self.WritePolymer(outfile,
  File "genpoly_lt.py", line 703, in WritePolymer
    self.ChooseDirections(coords)
  File "genpoly_lt.py", line 605, in ChooseDirections
    self.direction_vects[0][d] = coords[1][d] - coords[0][d]
IndexError: list index out of range

My workflow is following the logic below.
a) Run: python3 moltemplate_files/sequence_generator.py CH3 CH2 8405 41 41 40

import sys

def sequence(mon_lst, pol_deg, dims_lattice, random= False):
    """
        Função para a geração das sequências de monômeros que serão adicionadas
        ao polímero simulado. Esta função deve receber uma lista com os 
        monômeros declarados na forma de strings na lista, o grau de 
        polimerização, e as dimensões X, Y e Z da rede onde serão realizadas as 
        simulações. 

        Parâmetros:
        ·mon_lst: Lista com monômeros para a geração da sequência, cada monômero
            deve possuir o formato "CH2" ou "CH3" por exemplo. O primeiro valor
            da lista será tratado como "cap"; primeiro e último monômero de 
            cada polímero. O segundo será entendido como composto intermediário
            para a cadeia. Nesta versão, se monômeros adicionais forem 
            adicionados então serão ignorados, em versões futuras desse código, 
            será implementada uma regra para a geração de listas de
            heteropolímeros.
        
        ·pol_deg: Inteiro com o grau de polimerização da cadeia. 
        ·dims_lattice: Lista com três elementos inteiros informando o número de 
            sítions respectivamente nas direções 'X', 'Y' e 'Z' do volume 
            simulado. 
        ·radom: Variável booleana que em versões futuras será utilizada para 
            determinar se a colocação de monômeros alienígenas em 
            heteropolímeros será randômica (True) ou padronizada (False).

    """
    try:
        num_sitios = dims_lattice[0] * dims_lattice[1] * dims_lattice[2]
        num_cadeias = num_sitios // pol_deg
        pol_cap, pol_body = mon_lst[0], mon_lst[1]
    except:
        return ValueError

    with open("cuts.txt", 'w') as f:
        line = 0
        with open("sequence.txt", 'w') as file:
            for i in range(num_cadeias):
                file.write(pol_cap + "\n")
                line+=1
                for j in range(pol_deg-2):
                    file.write(pol_body + "\n")
                    line+=1
                file.write(pol_cap + ".rot(180,0,0,1)" + "\n")
                line+=1
                f.write(f"{line}\n")
def main():
    mon_lst = sys.argv[1:3]
    sys.argv[3:7] = [int(i) for i in sys.argv[3:7]]
    pol_deg, dims_lattice =  sys.argv[3], sys.argv[4:7]
    try:
        sequence(mon_lst, pol_deg, dims_lattice)
    except ValueError:
        print("**** ERRO ****\n", "Parâmetros inválidos!")
        exit()
    print("Sequencias de monômeros e de cortes geradas com sucesso!")
if __name__ == "__main__":
    main()

and
b) Run: ./lattice_generatos.sh

#!/bin/bash
cwd=$(pwd)		  # salva o diretório atual

POL_CAP='CH3';       	# Extremidade dos polímeros
POL_BODY='CH2';       # Corpo do polímero, heteropolímeros serão implementados
						# em outras versões do sequence_generator.py

#						
NMONOMERS=8405;         # O número de monômeros HDPE2911 8553 no entanto, 
						# para a modelagem e organização da rede em formato 
						# paralelepípedico, este valor não é factível, optou-se
						# por reduzir o GD para 8405 e adcioná-lo a uma rede de
						# 40 41 41
						# Para essa definição foi utilizada a seguinte 
						# metodologia:
						# 8553 * 8 (numero cúbico) = 68424
						# raiz(68424,3) = 40,901 -> 40
						# 68424 / 40 = 1710,6 -> 1710
						# raiz(1710,2) = 41,352 -> 41 
						# Logo a rede possui 41x41x40 = 67240 sítios que 
						# segmentados em oito unidades poliméricas resulta em
						# um gd de 67240/8 = 8405  



B=1.5350                # comprimento de cada monômero
DENSITY=0.96;		  	# densidade do polímero
MOL_WEIGHT=120000	

Nx=41; Ny=41; Nz=40;    # numero de sites (locais para a existência de uma 
						# partícula) da rede .

sites=$Nx*$Ny*$Nz;

# Gera a rede
cd ndmansfield/src/
./ndmansfield -box $Nx $Ny $Nz -seed 0 -tstart 1 -tsave 2000 -tstop $sites > curve_lattice.raw
mv curve_lattice.raw $cwd
cd $cwd


# Interpolação e reescalonamento da rede
SCALE=`echo "($NMONOMERS*$B)/($Nx*$Ny*$Nz-1)" | bc -l`   #comprimento da cadeia / #número de sites
python3 interpolate_curve.py $NMONOMERS $SCALE < curve_lattice.raw > curve_smooth.raw

# Transferência de arquivos
mv curve_smooth.raw curve_lattice.raw cuts.txt sequence.txt moltemplate_files/
cd moltemplate_files/

# Criação das sequências de monômeros e cortes
#/sequence_generator.py $POL_CAP $POL_BODY $NMONOMERS $Nx $Ny $Nz

# Criação do inputs LAMMPS 
python3 genpoly_lt.py	-polymer-name 'HDPE2911'\
						-monomer-name 'alcano'  \
						-sequence 'sequence.txt'\
						-bond Backbone C C  \
						-header 'import "compass_published.lt"'\
        				        -header 'import "ch2group.lt"' \
						-header 'import "ch3group.lt"' \
						-cuts 'cuts.txt' \
						< curve_lattice.raw > hdpe2911.lt

rm curve_smooth.raw curve_lattice.raw cuts.txt sequence.txt
#moltemplate.sh ...
cd $cwd

All files can be found here:
files.zip

Hello, Andrew.
I'm a student who just started using moltemplate. I found that the examples in official website of moltemplate do not include crystal construction, such as hexagonal crystal of SiC. This confuses me, and I can't build it after looking for many methods. Can you give me a simple example for me to learn? Please reply me, thank you very much.

Hello there,

When trying to generate data file using gaff.lt, I see a lot of redundant impropers being generated. This seems to be a problem with sorting atoms as I have been able to sort the output and see that the distinct atom sets equal the number of sp2 atoms.

Dear Author：

An error occured. I used "pip3 install moltemplate" to install latest version, then I typed "moltemplate.sh system.lt" and it told me that :

moltemplate.sh v2.17.10 2020-6-12

Traceback (most recent call last):
File "/home/roy/.local/bin/lttree_check.py", line 6, in
from pkg_resources import load_entry_point
File "/usr/lib/python2.7/dist-packages/pkg_resources/init.py", line 3088, in
@_call_aside
File "/usr/lib/python2.7/dist-packages/pkg_resources/init.py", line 3072, in _call_aside
f(*args, **kwargs)
File "/usr/lib/python2.7/dist-packages/pkg_resources/init.py", line 3101, in _initialize_master_working_set
working_set = WorkingSet._build_master()
File "/usr/lib/python2.7/dist-packages/pkg_resources/init.py", line 574, in _build_master
ws.require(requires)
File "/usr/lib/python2.7/dist-packages/pkg_resources/init.py", line 892, in require
needed = self.resolve(parse_requirements(requirements))
File "/usr/lib/python2.7/dist-packages/pkg_resources/init.py", line 778, in resolve
raise DistributionNotFound(req, requirers)
pkg_resources.DistributionNotFound: The 'moltemplate==2.17.10' distribution was not found and is required by the application.

And i tried sudo pip3 but also failed.

When i git clone the source code from github, and use both "pip3 install . " and "pip3 install --user .", but:

moltemplate.sh v2.17.10 2020-6-12

Traceback (most recent call last):
File "/home/roy/.local/bin/lttree_check.py", line 5, in
from moltemplate.lttree_check import main
ImportError: No module named moltemplate.lttree_check

So i dont know what's wrong. I will try old version to check if those mistakes is owe to my fault.

We've discussed this already in sgsaenger/vipster#35,
but here are some ideas i have about the architecture of your scripts.
I've mostly looked at ltemplify.py, so this is centered around this file.

It seems like the different workloads of ltemplify.main() are separated into logical blocks already.
These could easily be encapsulated in functions to increase interoperability/readability, e.g. like

def main():
    parse_pass1()
    parse_pass2()
    eval_atoms()
    eval_masses()

This usually decreases statefulness and makes it easier to export an API.

More importantly, i'd recommend using something like argparse to handle cmdline-arguments.
I've stumbled over this because ltemplify.py itself does not tell you about the (semi-mandatory?) use of the -atom_style argument.
argparse would add a -h option for free, which greatly improves discoverability.

Semi-related to this (just don't want to spam issues), would it be possible to parse the atom_style comment from the Atoms section? At least, comments like in moltemplate.sh about the guessed/default atom_style should be printed.

Thank you very much for the great work! I am trying to build an lt file for the Sodium dodecyl sulfate (SDS) molecule. When I checked the lt file, there is no atom type that corresponds to the elements (C, O, S) in the charged head group of SDS system. After a deep online search, I found some useful papers (see link below) with relevant information about its LJ parameters (and others). Is it possible for you to help add them to the oplsaa.lt or guide me on how to go about it? Thanks.

https://pubs.acs.org/doi/10.1021/acs.jctc.7b00181

https://pubs.acs.org/doi/full/10.1021/acs.jctc.9b00947

EDIT
When I originally posted this issue on 2021-4-08, I was worried that DREIDING-style hydrogen-bond interactions might not work in moltemplate due to the way atoms are ordered. Today, I attempted to address the root cause of the problem. I tried editing the code included with moltemplate (specifically the "postprocess_input_scripts.py" file) to make sure it can understand the syntax of "hbond/dreiding" pair_coeff commands. When I did that, I realized that the code already does this (and has done this since before 2019/11/11). But this was buried deep in the code, and I did not remember I had this working when I created this issue. So, assuming the code works, the original concern I had when I created this issue is largely moot. I'm sorry if I caused unnecessary concern.

However Matt Bone has since contacted me to bring up another possible problem that occurs when two different atom types can be both hydrogen-bond donors and acceptors. (See example below.) This is a different but closely related problem, so I included it here as well. To address this problem, we may need to add some additional atom types to the "dreiding.lt" file and do some testing.

Here is the original post. It is probably no longer relevant, but I will leave it up until we have confirmed that everything is working and all of these issues have been resolved. -A 2022-2-09*

The DREIDING force field occasionally makes use of pair_style hbond/dreiding/lj.

• In the "dreiding.lt" file, in each corresponding pair_coeff command for these interactions, we are assuming that the first atom type is a hydrogen bond donor, because we invoke the pair_coeff command using the "i" argument. For details, see the documentation for pair_style hbond/dreiding/lj.
• However all pair_coeff i j... commands requires that i≤j. (See the documentation for pair_coeff.)
• To comply with this requirement, moltemplate.sh actually has a post-processing step where it looks inside all of the pair_coeff commands and swaps the order of the atom types whenever i>j. When it does this, it only considers the i and j numbers (after the @atom types have been converted into numbers). It does not know whether i or j correspond to donor or acceptor atom types.
• In moltemplate, by default, @atom types are assigned to numbers according to the order in which they first appear in any of the user's LT files. Currently (as of 2021-4-08), the donor atom types (@atom types ending in "_hd") are interspersed with with the acceptor atom types (ending in "_ha").
• This means that, approximately half of the time, LAMMPS will confuse the donor and acceptor atoms in each hbond/dreiding/lj interaction.

There are two solutions to this problem:

1) Edit the postprocess_input_script.py and postprocess_coeffs.py files and make them aware of the quirks of the hbond/dreiding/ pair_coeff syntax.

2) Modify the "dreiding.lt" file to make sure all of the donor atom types are mentioned before any of the acceptor atom types. This is the easiest solution, and it works nearly all of the time. But it will fail if the user decides to override the @atom number assignments (by invoking moltemplate.sh using either the "-a" or "-b" arguments on those atom types). It will also fail in the unlikely event that users decide to refer to an acceptor atom (eg "@atom:N_R_b1_d2_ha") somewhere at the very beginning of their LT file, before the import "dreiding.lt" command is issued (causing it to be assigned to 1).

For now (2021-4-08), I will try solution 2. Later, I will try solution 1 when I have more time.
Meanwhile, I will leave this issue on the tracker until it is resolved.

EDIT
I have implemented both solutions 1 and 2. We just need to make some changes to the "dreiding.lt" file and test to make sure everything works. -A 2022-2-09

As atomic charges can be obtained from ab initio calculations, it might be desired sometimes to use charges explicitly given in the molecule LT file even in the case of OPLS-AA, for example, for some experimental purposes of testing. Could this be easily achieved in the present version?

Thank you very much for your great work.

Dear Andrew,

I'm wondering if there's an easy way to fill up the specified simulation box with particles.

I tried many ways of manipulating this matrix but I either get arrangments that are too small or outside the simulation box.

Thank you for your help.

Best regards,
Yunes Salman