How to run MMGBSA with OpenMM? about ambertools-openmm-md HOT 13 CLOSED

MMPBSA.py will be included automatically in the PATH if you have installed Ambertools.
For example, on Google Colab, you can do

1. Install conda

!pip install condacolab
import condacolab
condacolab.install_mambaforge()

2, Install Ambertools

!mamba install -c conda-forge ambertools -y

3, source the home directory of ambertools

amberhome = "source /usr/local/amber.sh"

4, check now MMPBSA.py should be working

!MMPBSA.py -h

It would be very similar when doing this on any local Linux.

Quantao

from ambertools-openmm-md.

Hi,

I run as your guide but it said:

I installed ambertools by using conda with version 23.3:

It was supposed to be an error since we haven't provided any input like mmpbsa.in file etc. It all looks good, just try to run a complete job with all proper input files MMPBSA.py needed. ante-MMPBSA.py should be already there as well.

from ambertools-openmm-md.

Hi,
Sorry for the late reply.
In the example above, we still use Amber's mmpbsa.py to run the job.
OpenMM is able to run the Amber input by directly reading *prmtop and *inpcrd files.

from simtk.openmm import *
from simtk.openmm.app import *
from simtk.unit import *

# Input Files

prmtop = AmberPrmtopFile('complex.prmtop')
inpcrd = AmberInpcrdFile('complex.inpcrd')

So it is still exactly the same way as how Amber runs MMPBSA if you were familiar with Amber.
The two complex.prmtop and complex.inpcrdis expected to be generated from scratch or with some third-party web servers like Charmm GUI.

When using Charmm Gui, the output format may be a bit different, just replacing the two files with the equivalent one should be fine.

from ambertools-openmm-md.

Thank you for your reply.

I couldn't find two python scripts in your code: MMPBSA.py and ante-MMPBSA.py.

Please show me them. Thank you very much.

from ambertools-openmm-md.

Thank you very much. How about ante-MMPBSA.py?

from ambertools-openmm-md.

Hi,

I run as your guide but it said:

I installed ambertools by using conda with version 23.3:

from ambertools-openmm-md.

Hi,
I am trying to prepare the ligand following your instruction to generate tleap. But I could not solve the bellow problem:

Could you please show me the way to figure out?

from ambertools-openmm-md.

This is my ligand and protein files:
https://drive.google.com/file/d/1_IH-GCgc8r3pN7qAgEBfKodbl9jCceGn/view?usp=share_link
https://drive.google.com/file/d/150q-7tIq5A-xCQZXcvxSToiEx7LpOlS9/view?usp=share_link

from ambertools-openmm-md.

from ambertools-openmm-md.

Hi @quantaosun,

When I run this cell:

!ante-MMPBSA.py  -p complex.prmtop -c com.prmtop -r rec.prmtop -l ligand.prmtop -s :WAT:Na+:Cl-:Mg+:K+ -n :LIG --radii mbondi2

It said that:

Traceback (most recent call last):
  File "/usr/local/bin/ante-MMPBSA.py", line 82, in <module>
    parmed = which('parmed', search_path=True)
  File "/usr/local/lib/python3.10/site-packages/MMPBSA_mods/findprogs.py", line 71, in which
    amberhome = get_amberhome()
  File "/usr/local/lib/python3.10/site-packages/MMPBSA_mods/findprogs.py", line 62, in get_amberhome
    raise MMPBSA_Error('AMBERHOME is not set!') 
MMPBSA_mods.exceptions.MMPBSA_Error: AMBERHOME is not set!

And, when I run this cell: !MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA_decomposition.dat -sp complex.prmtop -cp com.prmtop -rp rec.prmtop -lp ligand.prmtop -y prot_lig_prod_all.dcd, it throws:

Traceback (most recent call last):
  File "/usr/local/bin/MMPBSA.py", line 41, in <module>
    from MMPBSA_mods import main
  File "/usr/local/lib/python3.10/site-packages/MMPBSA_mods/main.py", line 43, in <module>
    from MMPBSA_mods.commandlineparser import parser
  File "/usr/local/lib/python3.10/site-packages/MMPBSA_mods/commandlineparser.py", line 60, in <module>
    default=os.path.join(os.getenv('AMBERHOME'), 'dat', 'mmpbsa',
  File "/usr/local/lib/python3.10/posixpath.py", line 76, in join
    a = os.fspath(a)
TypeError: expected str, bytes or os.PathLike object, not NoneType

Please help me to fix them. Thank you very much.

from ambertools-openmm-md.

Hi @quantaosun,

When I run this cell:

!ante-MMPBSA.py  -p complex.prmtop -c com.prmtop -r rec.prmtop -l ligand.prmtop -s :WAT:Na+:Cl-:Mg+:K+ -n :LIG --radii mbondi2

It said that:

Traceback (most recent call last):
  File "/usr/local/bin/ante-MMPBSA.py", line 82, in <module>
    parmed = which('parmed', search_path=True)
  File "/usr/local/lib/python3.10/site-packages/MMPBSA_mods/findprogs.py", line 71, in which
    amberhome = get_amberhome()
  File "/usr/local/lib/python3.10/site-packages/MMPBSA_mods/findprogs.py", line 62, in get_amberhome
    raise MMPBSA_Error('AMBERHOME is not set!') 
MMPBSA_mods.exceptions.MMPBSA_Error: AMBERHOME is not set!

And, when I run this cell: !MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA_decomposition.dat -sp complex.prmtop -cp com.prmtop -rp rec.prmtop -lp ligand.prmtop -y prot_lig_prod_all.dcd, it throws:

Traceback (most recent call last):
  File "/usr/local/bin/MMPBSA.py", line 41, in <module>
    from MMPBSA_mods import main
  File "/usr/local/lib/python3.10/site-packages/MMPBSA_mods/main.py", line 43, in <module>
    from MMPBSA_mods.commandlineparser import parser
  File "/usr/local/lib/python3.10/site-packages/MMPBSA_mods/commandlineparser.py", line 60, in <module>
    default=os.path.join(os.getenv('AMBERHOME'), 'dat', 'mmpbsa',
  File "/usr/local/lib/python3.10/posixpath.py", line 76, in join
    a = os.fspath(a)
TypeError: expected str, bytes or os.PathLike object, not NoneType

Please help me to fix them. Thank you very much.

Hi,

Have you run the following command before try mmpbsa ?

amberhome = "source /usr/local/amber.sh"
.

It looks like just due to you haven't set AMBERHOME variable.

from ambertools-openmm-md.

Hi @quantaosun, I run it, but there is still an error announced.

from ambertools-openmm-md.

I tried this command, it worked:

import os
os.environ['AMBERHOME'] = "/usr/local"
!echo $AMBERHOME
!source "$AMBERHOME/amber.sh"

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