[gmx-users] About Topology construction for CNT wrapped by Cyclic peptide

[Justin Lemkul]

On Wed, Apr 10, 2013 at 8:56 AM, vidhya sankar <scvsankar_agr at yahoo.com>wrote:

> Dear  Justin , Thank you for your reply,
>                                                                     I need
> to construct  Topology For Carbon Nano tubes (CNT) in  gromoff53a5.ff .
>
> For that  When i run the Following Command
>
>  ./g_x2top_d   -f CNT.gro   -o CNT.top  -r CNT.rtp
>
> I have got Error as follows
> Can not find forcefield for atom N-325 with 0 bonds
> Can not find forcefield for atom CA-326 with 2 bonds
> Can not find forcefield for atom CB-327 with 2 bonds
> Can not find forcefield for atom CG-328 with 2 bonds
> Can not find forcefield for atom C-330 with 2 bonds
> Can not find forcefield for atom O-331 with 1 bonds
> Can not find forcefield for atom N-332 with 0 bonds
>

The preceding lines appear to belong to a protein residue. Don't use
g_x2top for proteins. That's what pdb2gmx is for.


> Can not find forcefield for atom C-836 with 3 bonds
> Can not find forcefield for atom C-837 with 3 bonds
> Can not find forcefield for atom C-838 with 2 bonds
> Can not find forcefield for atom C-839 with 2 bonds
> Can not find forcefield for atom C-840 with 3 bonds
> Can not find forcefield for atom C-841 with 3 bonds
> Can not find forcefield for atom C-842 with 2 bonds
> Can not find forcefield for atom C-843 with 2 bonds
>
> Could only find a forcefield type for 321 out of 843 atoms
>
>
> How to solve it ?
>

You need a suitable .n2t file. For a CNT, it is trivial to create the
necessary entry since the geometry is regular. Please consult the manual
and website.

-Justin

-- 

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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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