[Question]: GromacsError: Only 3-point vsite type 1 is supported

[huaiaee]

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]

(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]

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

[marioernestovaldes]

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

[huaiaee]

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]

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]

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]

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)