[gmx-users] addition of the .itp file of a new residue

soumadwip ghosh soumadwipghosh at gmail.com
Thu Nov 20 06:43:11 CET 2014

Dear all,
             I have generated a .itp file for tetramethyl ammonium ion
(tma) for my system as advised by Dr. Justin. I copied this to my working
directory of GROMACS where I have the tma.pdb file as well. I did the

1. did pdb2gmx -f dna.pdb -o init.gro,
2. added the tma.itp file in the topology file as below-

;       File 'topol.top' was generated
;       By user: onbekend (0)
;       On host: onbekend
;       At date: Wed Nov 19 22:50:17 2014
;       This is a standalone topology file
;       It was generated using program:
;       pdb2gmx - VERSION 4.5.6
;       Command line was:
;       pdb2gmx -f 1.pdb -o init.gro
;       Force field was read from the standard Gromacs share directory.

; Include forcefield parameters
#include "charmm27.ff/forcefield.itp"
#include "tma.itp"

; Include chain topologies
#include "topol_DNA_chain_A.itp"
#include "topol_DNA_chain_B.itp"

; Include water topology
#include "charmm27.ff/spce.itp"

; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000

; Include topology for ions
#include "charmm27.ff/ions.itp"

[ system ]
; Name
GROtesk MACabre and Sinister

[ molecules ]
; Compound        #mols
DNA_chain_A         1
DNA_chain_B         1

then I am doing editconf, followed by genbox,
I intend to add tma first in the system, so I use-
genbox -cp box.gro -ci tma.pdb -nmol 22 -p topol.top -o box_tma.gro

but .top file is showing-

[ molecules ]
; Compound        #mols
DNA_chain_A         1
DNA_chain_B         1
there is no tma (22) added in the .top file. If this step is successful, I
wish to call genbox again to fill the rest of the box with water.

Am I writing the #include section wrongly?
Do I need to do anything else?

Any kind of help will be hugely appreciated.


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