[gmx-users] how to generate .top file
tsjerkw at gmail.com
Fri May 23 12:15:09 CEST 2014
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
[ moleculetype ]
[ 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.
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Tsjerk A. Wassenaar, Ph.D.
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