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

Justin A. Lemkul jalemkul at vt.edu
Wed May 9 14:38:55 CEST 2012

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 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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