[gmx-users] Re:Re: CNT

trevor brown trevorbrown34 at gmail.com
Tue Jan 18 20:57:17 CET 2011

Dear Mark,
Do you mean I will obtain 2 seperate .itp files for CNT and peptide. And
I already have spc.itp. Then I will write a short .top file which only
consists of include files.
Is that all what I will do?

In addition, I think I should combine pdbs od CNT and peptide by pymol,VMD

best wishes

On 18/01/2011 10:25 AM, trevor brown wrote:
> Dear friends,
> I have constructed a .top file for a CNT by g_x2top. to do this I
> have added C-C interactions in .n2t file and also related ff in
> .atomtypes.atp. I have also a .top file for a peptide by pdb2gmx.
> My aim is to construct a simulation system in which I want to see the
> adsorption.
> I don't know the next steps, could you guide me for further steps?

You need to end up with a .top file that has the logical structure of

#include force field files
#include CNT.itp
#include peptide.itp
#include solvent.itp

Peptide 1
SOL 10000

and a coordinate file whose molecules are ordered exactly as in the
above field, and whose atoms within molecules are ordered exactly as in
the [atoms] fields in the .itp file. Your molecule names must match
those given in the .itp files.

See the examples in section 5.7.1-5.7.3 of the manual.


> My second question; I have .gro and .tp files for both CNT and
> peptide, do I need any other files such as .itp or .ndx?
> Last question: Do you have such a tutorial?
> best wishes
> trevor
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