GROMACS version:2018
GROMACS modification: No
Dear Justin
I am trying to run md simulation on a complex composed of a protein with an unnatural residue (FGL) and a small organic molecule (SGC).So I reffered to SwissSidechain - A database of non-natural sidechains server to apply charmm27 force field to run MD on free protein with formyl glycine residue (FGL) . MD simulation was done successfully on free protein. Then, I reffered to https://www.swissparam.ch/ to obtain all required topology files to run MD simulation on complex. All the steps I did are:
SGC.mol2 file with all hydrogen atoms was obtained from UCSF chimera, then uploaded in https://www.swissparam.ch/ to obtain topology and parameters for SGC molecule compatible with the CHARMM27 all atoms force field. finally, complex.gro and modified topol.top were generated
This is my modified topol.top file generated by pdb2gmx;
; :-) GROMACS - gmx pdb2gmx, 2016.4 (-:
;
; Executable: /usr/local/gromacs/bin/gmx
; Data prefix: /usr/local/gromacs
; Working dir: /media/vaio/Apacer PHD/ARSA/docking results/SGC/WT
; Command line:
; gmx pdb2gmx -f ARSA.pdb -o ARSA.gro -ignh
; Force field was read from current directory or a relative path - path added.
;
; Include forcefield parameters
#include “./charmm27.ff/forcefield.itp”
; Include chain topologies
#include “SGC.itp”
#include “topol_pro_chain_A.itp”
; Include water topology
#include “./charmm27.ff/tip3p.itp”
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include topology for ions
#include “./charmm27.ff/ions.itp”
[ system ]
; Name
Protein in water
[ molecules ]
; Compound #mols
Protein_chain_A 1
SGC 1
SOL 18250
When I issued the gmx grompp -f ions.mdp -c complex-solv.gro -p topo.top -o ions.tpr
I face this warnings:
NOTE 1 [file ions.mdp]:
With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
that with the Verlet scheme, nstlist has no effect on the accuracy of
your simulation.
Setting the LD random seed to 1794072544
WARNING 1 [file SGC.itp, line 11]:
Overriding atomtype C=C
WARNING 2 [file SGC.itp, line 17]:
Overriding atomtype SO2
Generated 28441 of the 28441 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 25311 of the 28441 1-4 parameter combinations
I saw the SGC.itp file to check if C=C and SO2 atomtypes were not defined more than one time in directive [atomtype] but did not find anything strange there.
I would be grateful if you help me to solve this problem.
Please let me know if it is required to send SGC.itp file.
Thanks in advanve
Farial