[gmx-users] Error while using forcefield GROMOS 43a1p

Justin A. Lemkul jalemkul at vt.edu
Sat Nov 27 04:48:22 CET 2010

Jignesh Patel wrote:
> Dear Justin,
> I am trying to do simulation of a system which contains phosphorylated 
> serine using  GROMOS 43a1p forcefield. While running pdb2gmx command, I 
> am getting following error.
> Fatal error:
> Atom N not found in residue seq.nr <http://seq.nr>. 1 while adding improper

Well, either the N atom of residue 1 is not present in your .pdb file (in which 
case you've got a broken structure that needs fixing), or something else is 
going on.  Without seeing the contents of your input coordinate file (just the 
first residue, really) and your pdb2gmx command line, there's not much help 
anyone can give you.


> thank you in anticipation.
> With regards,
> Jignesh Patel


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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