Some pdb files can not work via GROMACS

[pelinsu]

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Hi all, i am a new person for GROMACS. when I try to use tutorial 5(protein-ligand complex) I had some weird error in the topology and energy minimization part. originally my protein has 7 chains but I want to use only 2 chains of 7 chains. before to start gromacs I made some preprocess via chimera (I deleted solvent, ligand and other 5 chains). but when I try to make topol.top I got this error:

Fatal error:

Atom HB3 in residue MET 1 was not found in rtp entry MET with 19 atoms

while sorting atoms.

For a hydrogen, this can be a different protonation state, or it

might have had a different number in the PDB file and was rebuilt

(it might for instance have been H3, and we only expected H1 & H2).

Note that hydrogens might have been added to the entry for the N-terminus.

Remove this hydrogen or choose a different protonation state to solve it.

Option -ignh will ignore all hydrogens in the input.

and later on, I used -ignh but in that case my topol.top file does not seems well. it seems:

This is a standalone topology file
;
; Created by:
; :-) GROMACS - gmx pdb2gmx, 2021.4-Homebrew (-:
;
; Executable: /usr/local/bin/…/Cellar/gromacs/2021.4/bin/gmx
; Data prefix: /usr/local/bin/…/Cellar/gromacs/2021.4
; Working dir: /Users/…/Desktop/kodaMD
; Command line:
; gmx pdb2gmx -f …pdb -o …_processed.gro -ter -ignh
; Force field was read from the standard GROMACS share directory.
;

; Include forcefield parameters
#include “charmm27.ff/forcefield.itp”

; Include ligand parameters
#include “LIG.itp”

; Include chain topologies
#include “topol_Protein_chain_A.itp”
#include “topol_Protein_chain_B.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
Protein_chain_B 1
LIG 1
SOL 24721

[jalemkul]

That’s a normal topology for a multi-chain system. pdb2gmx will, by default, write the topology of each protein chain to its own .itp file.

Note that if you are using the tutorial’s approach to parametrize the ligand with CGenFF, it will not work in conjunction with the charmm27.ff files provided with GROMACS. You need to get the CHARMM36 port from Alex MacKerell’s site and generate the protein topology with that.

[pelinsu]

Hi, thank you.

I am always getting rmsd graphs that have very fluctuated for both protein or protein-ligand simulations.when I checked via VMD I realized dimers are separated from each other.
if I add posre.A.itp and posre.B.itp lines for my topology files, is it work or not needed ? if it is not needed how can I solve?

this is protein in water for 50 ns

this is protein-ligand for 5 ns

this protein-ligand for 100 ns