selection syntax

[Jameel9]

Hi all,

There used to be some sort of an example that show how to select specific residues or nucleotides to be treated as ligand instead of the entire chain/group. I am sure I saw that years ago in one of the instructoins.in files but couldn't find it now.

Suppose you have a protein-DNA complex, and you just want to treat specific nucleotides as the ligand and the protein as the receptor. What would be the correct syntax?

[Valdes-Tresanco-MS]

The receptor and ligand should be independent molecules. But if you want to carry out the calculation, gmx_MMPBSA is quite flexible, although I cannot guarantee you will get good results. In this case, create a group containing the residues you want and use it as the ligand

gmx make_ndx -n index.ndx -f md.tpr
# create the ligand group using residue selection
r 10-20 22
# reconfigure the receptor group
(rec group) 1 &! 19 (ligand group or r 10-20 22)

[Jameel9]

Hi @Valdes-Tresanco-MS
Thank you for your help.

Sorry for the late reply. I did created a new index group containing the part of nucleic acid I am interested in and tried to run the calculations. Unfortunately, it didn't work and the tool seems to match the total number of atoms with the .itp files. The following is the output from the terminal

(gbsa) PC@PC-Precision-3460:~/complex/prot1/MMGBSA/trimmedDNA$ ./run.sh 
[INFO   ] Starting gmx_MMPBSA 1.6.4
[INFO   ] Command-line
  gmx_MMPBSA -O -i instructions.in -cs production_run.tpr -ci index_new.ndx -cg 1 22 -ct corr_trajectory.xtc -cp topol.top

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

[INFO   ] Checking exteDNAl programs...
[INFO   ] cpptraj found! Using /home/PC/miniconda3/envs/gbsa/bin/cpptraj
[INFO   ] tleap found! Using /home/PC/miniconda3/envs/gbsa/bin/tleap
[INFO   ] parmchk2 found! Using /home/PC/miniconda3/envs/gbsa/bin/parmchk2
[INFO   ] sander found! Using /home/PC/miniconda3/envs/gbsa/bin/sander
[INFO   ] Using GROMACS version > 5.x.x!
[INFO   ] gmx found! Using /usr/local/bin/gmx
[INFO   ] Checking exteDNAl 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 Protein_trimmed_DNA (1_22) 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 Protein (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 trimmed_DNA (22) 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...
[ERROR  ] MMPBSA_Error 

The number of atoms in the topology (3327) and the complex structure (3298) are different. Please check these files and verify that they are correct. Otherwise report the error...

Check the gmx_MMPBSA.log file to report the problem.
  File "/home/PC/miniconda3/envs/gbsa/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
             ^^^^^^^^^^^
  File "/home/PC/miniconda3/envs/gbsa/lib/python3.11/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
    app.make_prmtops()
  File "/home/PC/miniconda3/envs/gbsa/lib/python3.11/site-packages/GMXMMPBSA/main.py", line 681, in make_prmtops
    self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
                                                                          ^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/PC/miniconda3/envs/gbsa/lib/python3.11/site-packages/GMXMMPBSA/make_top.py", line 125, in buildTopology
    tops = self.gmxtop2prmtop()
           ^^^^^^^^^^^^^^^^^^^^
  File "/home/PC/miniconda3/envs/gbsa/lib/python3.11/site-packages/GMXMMPBSA/make_top.py", line 569, in gmxtop2prmtop
    GMXMMPBSA_ERROR(f"The number of atoms in the topology ({error_info[1]}) and the complex structure "
  File "/home/PC/miniconda3/envs/gbsa/lib/python3.11/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
    raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error: 

The number of atoms in the topology (3327) and the complex structure (3298) are different. Please check these files and verify that they are correct. Otherwise report the error...

Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.