Regarding error while running gmx_MMPBSA

[Navneet Kumar]

Using CHARMM ff. 

Getting this error. 

gmx_MMPBSA -O -i mmpbsa.in -cs md_0_10.tpr -ci index.ndx -cg 1 14 -ct md_0_10_center.xtc -cp topol.top 

[INFO   ] Starting

[INFO   ] Checking external programs...

[INFO   ] cpptraj found! Using /home/pglab-5000/Downloads/amber20/bin/cpptraj

[INFO   ] tleap found! Using /home/pglab-5000/Downloads/amber20/bin/tleap

[INFO   ] parmchk2 found! Using /home/pglab-5000/Downloads/amber20/bin/parmchk2

[INFO   ] sander found! Using /home/pglab-5000/Downloads/amber20/bin/sander

[INFO   ] Using GROMACS version > 5.x.x!

[INFO   ] gmx found! Using /usr/local/gromacs-2018.8/bin/gmx

[INFO   ] Checking external programs...Done.

[INFO   ] Building AMBER Topologies from GROMACS files...

[INFO   ] Checking if supported force fields exists in Amber data...

[INFO   ] Get PDB files from GROMACS structures files...

[INFO   ] Making gmx_MMPBSA index for complex...

[INFO   ] Normal Complex: Saving group 1_14 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb

[INFO   ] No receptor structure file was defined. Using ST approach...

[INFO   ] Using receptor structure from complex to generate AMBER topology

[INFO   ] Normal Complex: Saving group 1 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb

[INFO   ] No ligand structure file was defined. Using ST approach...

[INFO   ] Using ligand structure from complex to generate AMBER topology

[INFO   ] Normal ligand: Saving group 14 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb

[INFO   ] Cleaning GROMACS topologies...

[INFO   ] Building Normal Complex Amber Topology...

  File "/home/pglab-5000/.local/bin/gmx_MMPBSA", line 8, in <module>

    sys.exit(gmxmmpbsa())

  File "/home/pglab-5000/.local/lib/python3.8/site-packages/GMXMMPBSA/app.py", line 97, in gmxmmpbsa

    app.make_prmtops()

  File "/home/pglab-5000/.local/lib/python3.8/site-packages/GMXMMPBSA/main.py", line 577, in make_prmtops

    self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()

  File "/home/pglab-5000/.local/lib/python3.8/site-packages/GMXMMPBSA/make_top.py", line 118, in buildTopology

    tops = self.gmxtop2prmtop()

  File "/home/pglab-5000/.local/lib/python3.8/site-packages/GMXMMPBSA/make_top.py", line 295, in gmxtop2prmtop

    com_top = parmed.gromacs.GromacsTopologyFile(self.complex_temp_top, xyz=self.complex_str_file)

  File "/home/pglab-5000/Downloads/amber20/lib/python3.8/site-packages/parmed/gromacs/gromacstop.py", line 259, in __init__

    self.coordinates = f.coordinates

  File "/home/pglab-5000/Downloads/amber20/lib/python3.8/site-packages/parmed/structure.py", line 1700, in coordinates

    coords = coords.reshape((-1, len(self.atoms), 3))

ValueError: cannot reshape array of size 18549 into shape (6184,3)

Exiting. All files have been retained.

[Mario Sergio Valdes]

Hello and welcome!

This error is related to the mismatch between the structure obtained with the defined groups and the topology. gmx_MMPBSA removes the waters and ions (Na and Cl) from the topology, so if you defined a group that contains them, then the structure and the topology will not match. Please review the PDB files that are generated for each group as well as the content of the groups you are defining.

Tell me if this solved the problem

Best!

Mario S.

[Mario Sergio Valdes]

I will create an issue on Github to fix this as it is frequent. However, it will have low priority

[Navneet Kumar]

Thank you for your response. 

Can you please elaborate hoe should I  proceeds. I mean what modifications exactly should I make? In topology file index file? 

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[Mario Sergio Valdes]

You do not have to make any modifications. gmx_MMPBSA is able to deal with almost all the elements in your topology, always they are named consistently.

Is your system Protein-Ligand?

Generally, the ligand group is 13 in these types of systems.

Check that the group you are defining corresponds exactly to the ligand, whether it is protein type or not

The error it reports occurs because parmed is trying to match the coordinates of the structure with the elements in the topology. If you define a group that contains waters or ions, such as gmx_MMPBSA removes them from the topology, then the structure will not match.

If you can't solve your problem, send me your system for review

Best!

Mario S.

[Navneet Kumar]

Yeah! 

Of course I m sure. Group 13 is metal ion. And 14 is small molecule. And as usual group 1 is protein. 

I will send you the detailed file by tomorrow. 

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[Mario Sergio Valdes]

Of course, send me the files to review. Extract only 10 frames from the trajectory, the tpr and the index files, and the receptor and ligand groups.

Best!

Mario S.

[Mario Sergio Valdes]

I have already identified the possible problem. Converting the topology from Gromacs to Amber is quite simple. The conversion works correctly if there are only 1 or 2 molecules in the [molecules] section of the topology other than Ions and Water. We will try to improve the conversion for the next version

Best!

Mario S

[Mario Sergio Valdes]

Hello.

The gmx_MMPBSA v1.4.1 is out. In this version we have fixed errors related to the processing of the topology, probably, the problem that you have reported will be solved. We invite you to update to the latest version and tell us how it went.

Best!

Mario S

[Navneet Kumar]

Thank you! Will update you soon.

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     Thanks & Regards

_______________________________________________________

NAVNEET KUMAR Doctoral Student Dept. of Pharmacoinformatics National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar - 160062, Punjab (INDIA) P +918017967647  |   E navne...@gmail.com  Please consider your environmental responsibility. Before printing this e-mail message, ask yourself whether you really need a hard copy.