[gmx-users] Go model -error in generating topology

[Justin A. Lemkul]

On 5/9/12 8:37 AM, mohan maruthi sena wrote:
> Hi all,
>            I try to build go model(which uses only c-alpha atoms), my pdb
> contains only c-alpha atoms extracted from the original pdb file ,when i use
> pdb2gmx command on c-alpha containing pdb file it gives the following error.
>
>              Atom N is used in an interaction of type atom in the topology
>            database, but an atom of that name was not found in residue
>              number 1.
> Please suggest me a way ,
>

pdb2gmx is not suited for building such a topology.

-Justin

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

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