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View Code? Open in Web Editor NEWLVPP sigma-profile database + COSMO-SAC parametrizations
License: MIT License
LVPP sigma-profile database + COSMO-SAC parametrizations
License: MIT License
Olá Rafael! Você poderia incluir a molécula Cyclopentyl methyl ether (CAS 5614-37-9, SMILE COC1CCCC1) no JCOSMO? Tenho usado suas referências em meus trabalhos de extração de óleo de soja utilizando solventes verdes:
https://doi.org/10.1016/j.jiec.2022.06.020
Atenciosamente! Abraço!
Hi,
Can you please help me understand the reason for different sigma profiles put out by GAMESS and Turbomole for the same molecule such as simple H2O (water) with the same DFT basis BP-TZVP? i have attached the two files for easy reference. The Turbomole file using BP-TZVP formulation was taken from the supply of: https://dx.doi.org/10.1021/acs.iecr.0c00449 which also contains a new BP-TZVPD formulation but that one can be different. This difference due to different DFT formulation was mentioned in: https://doi.org/10.3303/CET1543314
The averaged sigma profile over charge densities -2.5 to 2.5 is different as shown in the attached pic. The averaged profiles were generated using VT-2005 procedure.
WATER-GAMESS.txt
water_c0-Turbomole.TXT
I want to do the calculations for the riluzole drug and carbon dioxide.
I drew the structure through wxMacMolplt software and then converted it to (file.inp) with optimization and DFT calculation. Then, use from the OPENBABEL software, the file was converted to (file.mol) .The structure of two materials and (file.mol) is attached.
Please check if the 1,1,2-TRICHLOROETHANE conformation should be as here: https://webbook.nist.gov/cgi/cbook.cgi?Str3View=C79005&Type=JSmol
Please complete the database with more biodiesel related compounds like:
Not necessarily use the nomenclature considered in that paper.
Also fix some of the compounds currently without the underline, like: METHYLOLEATE, METHYLLINOLEATE and possibly others.
I would like to cite your repository in our upcoming paper, but the best way to do that is to have an archival release version with a DOI. Could you please mint a DOI for your release version so I can make direct reference to that particular release? Systems like zenodo make this process seamless.
Dear all,
looking through the list of GAMESS COSMO cavities, I stumbled across files that lack the cavity data.
I did not (!!) check all files manually that caused an issue, however the ones I did check by hand were indeed lacking the cavity data, which makes me suspect the same is true for the other files in the list.
This is the list I obtained:
1,2,3-TRIMETHYLBENZENE
1,4-DIMETHYLNAPHTHALENE
1,5-DIMETHYLNAPHTHALENE
1-BUTYNE
1-OCTYNE
2,3-PENTADIENE
2-BUTYNE-1,4-DIOL
2-HEPTYNE
2-HEXYNE
3-DECYNE
3-HEPTYNE
3-METHYL-1-HEXYNE
4-METHYL-1-HEXYNE
4-METHYL-1-PENTYNE
4-METHYL-2-HEXYNE
5-METHYL-1-HEXYNE
5-METHYL-2-HEXYNE
A-PINENE
ETHYLACETYLENE
ETHYL_CYANOACETATE
ETOSO3-1
FRUCTOSE
HEPTENE-6-NITRILES
HEXAMETHYLPHOSPHORAMIDE
IBUPROFEN
ISO-VALERONITRILE
LINALOOL
METHYLGLUTARONITRILE
MPY+1
PARACETAMOL
PENTANOIC_ACID
SACCHAROSE
TCB-1
The current D-Glucose molecule do not have the closed ring as described, e.g., here: https://en.wikipedia.org/wiki/Glucose
Please check if this is correct and possibly fix it.
Thank you in advance.
Please add the following CADs:
When I run scons with GAMESS appears error 1 and error 127. The files can not be found although they do exist.
Hello,
Im having a error message when running scons, it states that "
scons: Reading SConscript files ...
File "/home/anggawirya/sigma-master/GAMESS/SConstruct", line 102
print(len(gamess_version))
^
TabError: inconsistent use of tabs and spaces in indentation
do you know what might wrong in my case ? Many thanks
Hello! Could you help me?
Scons is returning error 1 when trying to generate the sigma profile.
I've tried to compute sigma-p for LACTIC_ACID.mol, using the mol file provided in the database.
It seems it computes the calculation up to the line:
/home/csrafaelcs/src/gamess/rungms LACTIC_ACID.inp > LACTIC_ACID.gamout
After this, I get an error: Illegal variable name.
And it ends with a error 1 from scons.
Complete terminal lines are:
scons: Reading SConscript files ...
LACTIC_ACID.gout
Delete([])
scons: done reading SConscript files.
scons: Building targets ...
/home/csrafaelcs/src/gamess/rungms LACTIC_ACID.inp > LACTIC_ACID.gamout
Illegal variable name.
scons: *** [LACTIC_ACID.gamout] Error 1
scons: building terminated because of errors.
Any solution?
Hello, I would like to request the inclusion of chlorophyll a and chlorophyll b in LVPP's sigma-profile database for COSMO-based models.
Files containing molecules with minimum energy structures are attached. Please verify your agreement with these structures since I found a variety of representations to the bonds with Mg in these molecules.
Best regards,
Allan Morcelli
Hello, I would like to request the Calculation and inclusion of melanoidins in LVPP's sigma-profile database for COSMO-based models. Attached are the 5 possible structures since the final structure has not yet been defined, thank you I appreciate any help.
Hello,
NA+1 present in the library is not supported by jcosmo, it displays the message 'Compound not found'. The problem is the same for a new gout file obtained with GAMESS.
Is it a normal issue?
Please find attached the gout files in .txt format.
NA+1_library.txt
NA+1_new.txt
Best,
Guillaume Simon
Chemical names are nice for humans, but less practical for computers.
It would be nice if the cavities were accompanied by a list of CAS numbers (asked for by many journals nowadays too), to uniquely identify each compound.
There is an online tool available - and I have been running the names through the tool. (This is the one I used: http://cts.fiehnlab.ucdavis.edu/ )
I did not (!) verify every match of name to CAS number, but I suspect between nothing or some errors, some errors are the lesser evil. In addition, I determined that using the cavities with the "regular sigma range" is not posible for ions. Radicals as well as some heavier atom also seem to cause issues.
Here is the 'result' of matching names to CAS numbers for the MOPAC cavities:
POA1_working_compounds.txt
POA1_ions_radicals_CAS_not_found.txt
Please add to the database the Quercetin molecule.
Details are available here: https://en.wikipedia.org/wiki/Quercetin
Hello Prof.Paula Bettio Staudt
I want to do the calculations for the riluzole drug and carbon dioxide.
I drew the structure through wxMacMolplt software and then converted it to (file.inp) with optimization and DFT calculation. Then, use from the OPENBABEL software, the file was converted to (file.mol) .The structure of two materials and (file.mol) is attached.
reregardingaboutcosmoactivitycoefficient (2).zip
Hello! I'm a newbie in COSMO calculations and I am trying to compute the sigma profiles using GAMESS by my own.
I've followed the tutorial and I have achieved to generate the .gout file for simple molecules like Lactic acid using GAMESS.
Then, I've tried to generate the .gout file for my molecule, praziquantel (). It worked very well but it demanded more than 10 hours to finish the calculations!
I would like to know if the calculations take this huge time to conclude normally?
I would be quite grateful if anyone could give me some tips to accelerate the calculations.
I tried to increase the memory changing the "kernel.shmmax" to 8000000000 and changing the MSWORDS (base.keys.gamess file) to 2000. But it takes more than 10 hours yet.
JCOSMO read my .gout file so I am considering that everything worked well. I appended the files if you want to check it.
Thanks.
S-PRAZIQUANTEL.zip
Hello, I would like to request the inclusion of some key carotenoids found in microalgae in LVPP's sigma-profile database for COSMO-based models.
all-trans-betacarotene
all-trans-lutein
all-trans-zeaxanthin
all-trans-violaxanthin
Files containing molecules with minimum energy structures are attached.
Best regards,
Allan Morcelli
Please add the gamma-valerolactone molecule to the database.
Further information is available at: https://en.wikipedia.org/wiki/Gamma-Valerolactone
The TCB-1 ion has the surface information missing for GAMESS and is wrong (exploded) for POA1
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