[gmx-users] Top file

[Justin A. Lemkul]

On 6/26/12 1:52 AM, Shima Arasteh wrote:
>   Dear gmx users,
>
>
> I have a problem about the topology output of pdb2gmx.
> There is a formyl residue as N-terminal in my .pdb file. I know that the pdb file is correct in agreement with RCSB .pdb files.
> The
>   force field I have to use is gmx ( I need to regenerate
>   some results ), so I defined the formyl residue as a new residue in gmx
>   force field. But when I get the output of pdb2gmx the topology shows
> that the N atom of the next residue has 3 H atoms ,I think It means that
>   the formyl residue is not connected to the next residue ( here: Valine
> ). As a result the total charge derived by pdb2gmx is +2e and it is not
> correct regards to
>   the protein structure. I don't know what is the problem? Is it related
> to the force field files?
>

Did you follow all of the instructions here?

http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

It also sounds like you are not setting termini properly using pdb2gmx -ter. 
Please provide your complete pdb2gmx command any any relevant screen output.

-Justin

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

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