[gmx-users] Re:Re: CNT

Justin A. Lemkul jalemkul at vt.edu
Tue Jan 18 20:59:53 CET 2011

trevor brown wrote:
> 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? 

Yes, you need topologies that describe all components of your system.

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

Yes, since you need a complete description of your system's coordinates in a 
single file.


> best wishes
> trevor
> 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
> [molecules]
> CNT 1
> 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.
> Mark
>  > 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


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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