[gmx-users] OPLS implicit solvent problems

[francesca.stanzione at unina.it]

   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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