Hello,
I try to perform an implicit solvent simulation with Gromacs 4.5.3.
version. I have a system corresponding to 6 peptides generated by
Pymol with simmetrical cell, so I have a single PDB. I used OPLS-AA
and i put the N-and C- termini as NH2 and COOH. My topology file is
correct, and is all systems are included.
; Include forcefield parameters
#include "./oplsaa.ff/forcefield.itp" -------> in this .itp file is
included gbsa.itp
; Include chain topologies
#include "topol_Protein_chain_A.itp"
#include "topol_Protein_chain_B.itp"
#include "topol_Protein_chain_C.itp"
#include "topol_Protein_chain_D.itp"
#include "topol_Protein_chain_E.itp"
#include "topol_Protein_chain_F.itp"
; Include water topology
#include "./oplsaa.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 "./oplsaa.ff/ions.itp"
[ system ]
; Name
Protein
[ molecules ]
; Compound #mols
Protein_chain_A 1
Protein_chain_B 1
Protein_chain_C 1
Protein_chain_D 1
Protein_chain_E 1
Protein_chain_F 1
-----------------------------------------------------------------------------
When I start my simulations (md_start.mdp) in implicit solvent, i
have this fatal error:
GB parameter(s) missing or negative for atom type 'opls_912B'
GB parameter(s) missing or negative for atom type 'opls_267'
GB parameter(s) missing or negative for atom type 'opls_269'
GB parameter(s) missing or negative for atom type 'opls_268'
GB parameter(s) missing or negative for atom type 'opls_270'
Program grompp, VERSION 4.5.3
Source code file: grompp.c, line: 1123
Fatal error:
Can't do GB electrostatics; the implicit_genborn_params section of the
forcefield is missing parameters for 5 atomtypes or they might be
negative.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors.
----------------------------------------------------------------------------
Controlling these atoms they corresponding to:
opls_912B= the CA of N-terminal residue
opls_267= Co in COOH
opls_268= Oh in COOH
opls_269= Oc in COOH neutral
opls_270= H in COOH
----------------------------------------
in the file gbsa.itp in opls.ff directory these atoms missing. Now,
have I done something wrong? If is all ok, is it possible to create
these missing atoms in the gbsa.itp file?
thanx,
francesca stanzione
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