[gmx-users] how to generate .top file

[Tsjerk Wassenaar]

Hi Lovika,

Yes, you can

#include "gold.itp"

or something along those lines.

Cheers,

Tsjerk


On Fri, May 23, 2014 at 12:44 PM, Lovika Moudgil <lovikamoudgil at gmail.com>wrote:

> 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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-- 
Tsjerk A. Wassenaar, Ph.D.