[gmx-users] how to generate .top file

[Lovika Moudgil]

Thanks for reply Abhijit... .I will definitely try this .

Hey Tsjerk ... Is it possible , if I define all this in a different  .itp
and than define that .itp file in .top file ?????


On Fri, May 23, 2014 at 3:45 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> 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.
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