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

[Justin Lemkul]

On 11/20/14 12:43 AM, soumadwip ghosh wrote:
> 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
> following-
>
> 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"
>
> #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 "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?
>

You need to update [molecules] to reflect the addition of the 22 new TMA.  The 
only time genbox works magic is for water named SOL; it's hard-coded that way. 
Anything else is up to you.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================