[gmx-users] Re: How to add dihedral information from the GAFF topology

[Biswajit Gorai]

Dear Bipin,
Edit your topology file as:

###########################################
; Include forcefield parameters
#include "amber99sb-ildn.ff/forcefield.itp"

; Include chain topologies
#include "topol_Protein_chain_A.itp"
#include "topol_Ion_chain_A2.itp"

*#include "oct.itp"*

; Include water topology
#include "amber99sb-ildn.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 "amber99sb-ildn.ff/ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound        #mols
Protein_chain_A     1
Ion_chain_A2        1
*1-octanol         1
*
*SOL              8987*
#######################################

It may be helpful to you.

Biswajit
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