[gmx-users] Top file

[Shima Arasteh]

 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?

Please help me with your suggestions. I would appreciate you.

Sincerely,
Shima