Hi, I am about to do energy minimization but the above error occurred, I checked my .mdp file and .top file but could not find the problem.
TOP file
; Include forcefield parameters
#include "amber99sb.ff/forcefield.itp"
; Include water topology
#include "amber99sb.ff/tip3p.itp"
#include "topol_Protein_chain_A.itp"
#ifdef POSRES
#include "posre_Protein_chain_A.itp"
#endif
#include "topol_Protein_chain_B.itp"
#ifdef POSRES
#include "posre_Protein_chain_B.itp"
#endif
#include "topol_Protein_chain_C.itp"
#ifdef POSRES
#include "posre_Protein_chain_C.itp"
#endif
; Include topology for ions
#include "amber99sb.ff/ions.itp"
[ system ]
; Name
Protein
[ molecules ]
; Compound #mols
Protein_chain_A 1
Protein_chain_B 1
Protein_chain_C 1
I'll either get "posre_Protein_chain_A is redefined" or the same error if I experimentally edit the either files.
Hi Siti! This error means that you need to pass the file after "-r" flag while compiling with grompp. Please, see the reference for gromacs: https://manual.gromacs.org/archive/5.0.4/programs/gmx-grompp.html
I dont have any restraint.gro file. or is it okay to use the protein.gro file?@
Dear Siti,
You can use the same .gro file that contains the coordinates for the system.
best,
Felippe
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