[gmx-users] how to generate .top file

Tsjerk Wassenaar tsjerkw at gmail.com
Fri May 23 12:15:09 CEST 2014

Hi Lovika,

IIRC your gold is frozen, right? So you have a moleculetype definition for
one gold atom (atomtype, mass, charge). You can just put it in the .top
file after the #includes of the force field, like

#include "forcefield.itp"
#include "protein.itp"

[ moleculetype ]
AU          1

[ atoms ]
1       AU      1       UA          UA       1      0        196.96655

[ system ]
Protein with gold

[ molecules ]

Hmm, I wonder, should one account for the gravitational effects of gold.
Pretty heavy stuff :p



On Fri, May 23, 2014 at 11:39 AM, Lovika Moudgil <lovikamoudgil at gmail.com>wrote:

> Hi everyone..
> I have a .pdb file with protein and gold slab .Problem is I can generate
> .top file for  my protein with pdb2gmx but I want my slab in the same
> system .I can generate .gro file for both but what about .top file . Can
> any body help me with this issue .Thanks in advance.
> Regards
> Lovika
> --
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.

Tsjerk A. Wassenaar, Ph.D.

More information about the gromacs.org_gmx-users mailing list