Grompp needs a posre.itp file

User discussions
1

Hello every one!

I’m working with complexe composed wtih a protein with four chainand ligand. When I use pdb2gmx the program
creates 4 different itp posre files (posre_protein_chain_A.itp,
posre_protein_chain_B.itp and posre_protein_chain_G.itp posre_protein_chain_R.itp).

whenI use the comande line

gmx grompp -f NVT.mdp -c EM.gro -r EM.gro -p topol.top -n index.ndx -maxwarn 2 -o NVT.tpr

i get problem of posre.itp not found

Just some information regarding my system:

in the topol.top file I have the lines

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

; Include ligand topology
#include “LIG.itp”

; Include chain topologies
#include “topol_Protein_chain_B.itp”
#include “topol_Protein_chain_A.itp”
#include “topol_Protein_chain_G.itp”
#include “topol_Protein_chain_R.itp”

; Include Position restraint file
#ifdef POSRES
#include “posre.itp”
#endif

; Ligand position restraints
#ifdef POSRES
#include “posre_LIG.itp”
#endif

; 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”

grompp needs a posre.itp file there is solution please

GROMACS version:2022.6
GROMACS modification: No
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2

Could you copy-paste all the outputs from the command (these would be all the notes, warnings and errors that output onto the command line after entering the command)?

You could also try double-checking the topol file for each protein chain, the bottom of each file should state which position restraint is included, maybe there’s some mismatch between which position restraint files are listed and which are present.