Ligand gets fragmented after recentering / Need help

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1

GROMACS version: 2020
GROMACS modification: NO
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AFter successfully completing the simulations, we are trying to extract a single pdb frame from .xtc file.
For this we do recentering. The following are the commands:

  1. recentering command: gmx_mpi trjconv -s md_40ns.tpr -f md_40ns.xtc -o md_40ns_center.xtc -center -pbc mol -ur compact < ./recent.txt
  2. gmx_mpi trjconv -s md_40ns.tpr -f md_40ns_center.xtc -o 4PPF_2BA_outcomp3_40ns.pdb -dump 40 <./dump.txt`

After doing this, some times the ligand in the complex is found fragmented, some times it is fine with intact connectivity.

What could be the reason? Any interpretation w.r.t the unfavorable binding in the binding site?
During one simulation - fragmeted ligand appears. Same complex when repeated for simulation with same commands, the ligand is intact.

Please help explain the rational behind this behavior while using gromacs.
Thanks in advance,
Regards,
Partha

2

Hi Partha

Since no-one more expert has answered your question I will take a stab at it :) This is what has worked for me:

System prepared according to the Lemkul tutorial (Protein-Ligand Complex)

Files:
em_1.gro: Coordinates after initial (steepest descents) minimization.
md_1f_1.gro + md_1f_1.xtc: Structure and trajectory files after MD run
index_1d.ndx: Index file including definition of the Protein-ligand complex (Protein_SM1)

Procedure:

Extract protein_SM1 complex after initial minimization

gmx editconf -f em_1.gro -n index_1d.ndx -o ref_1.gro << eof
Protein_SM1
eof

Use trjconv to fix pbc problem

gmx trjconv -f md_1f_1.xtc -s em_1.gro -n index_1d.ndx -pbc nojump -o tmp_1.xtc << eof
Protein_SM1
eof

At this point you should be able to dump any frame you want.

Please let me know whether this does / does not work for you.

Good luck!

Guy