[gmx-users] how to generate .top file

[Tsjerk Wassenaar]

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

Cheers,

Tsjerk



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
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-- 
Tsjerk A. Wassenaar, Ph.D.