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Valdes-Tresanco-MS / gmx_MMPBSA

gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.
https://valdes-tresanco-ms.github.io/gmx_MMPBSA/
GNU General Public License v3.0
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[Question]: GromacsError: Only 3-point vsite type 1 is supported #522

Open huaiaee opened 4 months ago

huaiaee commented 4 months ago

My Question is...

When I was performing MMPBSA calculations for a ligand embedded in a membrane, I referred to the content in this link. After running this command, I encountered the following error. Can you help me resolve it? I am certain that my ligand does not contain LPH atoms.

huaiaee commented 4 months ago

(gmxMMPBSA) root@ubuntu:~/mmpbsa/top2# gmx_MMPBSA -O -i mmpbsa.in -cs md.tpr -ci index_new.ndx -cg 1 13 -ct md_center.xtc -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv [INFO ] Starting gmx_MMPBSA v1.6.3 [INFO ] Command-line gmx_MMPBSA -O -i mmpbsa.in -cs md.tpr -ci index_new.ndx -cg 1 13 -ct md_center.xtc -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv

[INFO ] Checking mmpbsa.in input file... [INFO ] Checking mmpbsa.in input file...Done.

[INFO ] Checking external programs... [INFO ] cpptraj found! Using /root/miniconda3/envs/gmxMMPBSA/bin/cpptraj [INFO ] tleap found! Using /root/miniconda3/envs/gmxMMPBSA/bin/tleap [INFO ] parmchk2 found! Using /root/miniconda3/envs/gmxMMPBSA/bin/parmchk2 [INFO ] sander found! Using /root/miniconda3/envs/gmxMMPBSA/bin/sander [INFO ] Using GROMACS version > 5.x.x! [INFO ] gmx found! Using /root/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx [INFO ] Checking external programs...Done.

[INFO ] Building AMBER topologies from GROMACS files... [INFO ] Get PDB files from GROMACS structures files... [INFO ] Making gmx_MMPBSA index for complex... [INFO ] Normal Complex: Saving group receptor_ligand (1_13) 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 Receptor: Saving group receptor (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 ligand (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb [INFO ] Checking the structures consistency... [INFO ] [INFO ] Using topology conversion. Setting radiopt = 0... [INFO ] Building Normal Complex Amber topology... File "/root/miniconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in sys.exit(gmxmmpbsa()) File "/root/miniconda3/envs/gmxMMPBSA/lib/python3.10/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa app.make_prmtops() File "/root/miniconda3/envs/gmxMMPBSA/lib/python3.10/site-packages/GMXMMPBSA/main.py", line 681, in make_prmtops self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology() File "/root/miniconda3/envs/gmxMMPBSA/lib/python3.10/site-packages/GMXMMPBSA/make_top.py", line 124, in buildTopology tops = self.gmxtop2prmtop() File "/root/miniconda3/envs/gmxMMPBSA/lib/python3.10/site-packages/GMXMMPBSA/make_top.py", line 565, in gmxtop2prmtop com_top = self.cleantop(self.FILES.complex_top, self.indexes['COM']['COM']) File "/root/miniconda3/envs/gmxMMPBSA/lib/python3.10/site-packages/GMXMMPBSA/make_top.py", line 854, in cleantop rtemp_top = parmed.gromacs.GromacsTopologyFile(ttp_file.as_posix()) File "/root/miniconda3/envs/gmxMMPBSA/lib/python3.10/site-packages/parmed/gromacs/gromacstop.py", line 346, in init self.read(fname, defines, parametrize) File "/root/miniconda3/envs/gmxMMPBSA/lib/python3.10/site-packages/parmed/gromacs/gromacstop.py", line 460, in read b, bt = self._parse_vsites3(line, molecule.atoms, params) File "/root/miniconda3/envs/gmxMMPBSA/lib/python3.10/site-packages/parmed/gromacs/gromacstop.py", line 785, in _parse_vsites3 raise GromacsError('Only 3-point vsite type 1 is supported') GromacsError: Only 3-point vsite type 1 is supported Exiting. All files have been retained.

huaiaee commented 4 months ago

the link is https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/examples/Protein_membrane_CHARMMff/

marioernestovaldes commented 4 months ago

Delete everything related to vsites from your topology and try again to see if that solves the issue

huaiaee commented 4 months ago

Sorry, I suddenly found that the topology file of the ligand contains LPH atoms. Strangely, when I tried to rebuild the index file, the atom did not appear when splitting the ligand. How should I handle this？

marioernestovaldes commented 4 months ago

without the files, it's hard to say what could be going wrong... start fresh with only the required files an follow the tutorial about LPH particles. if still the error persists, feel free to send the files you are using to see what's going wrong

huaiaee commented 4 months ago

Thank you for your answer. After deleting everything related to vsites, it seems to be running normally. There is another issue, the. dat file I output seems to be different from the sample file, missing the following line:
Using C2 Entropy Approximation: |
ΔG binding = -48.0704 +/- 2.1972 | # What should we do in this situation？

Valdes-Tresanco-MS commented 4 months ago

Do you define the c2_entropy parameter in the input file? (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/examples/Entropy_calculations/C2_Entropy/?h=c2_entropy#command-line)