[gmx-users] missing of methyl at N-terminal

Mark Abraham Mark.Abraham at anu.edu.au
Fri Nov 7 14:03:52 CET 2008

Bhawana Gupta wrote:
> thankyou for ur reply.
> exact error which i m getting, when running pdb2gmx command with the pdb 
> which i had taken from insightII is
> Program pdb2gmx, VERSION 4.0
> Source code file: pdb2gmx.c, line: 429
> Fatal error:
> Atom C in residue NH2 6 not found in rtp entry with 3 atoms
>              while sorting atoms

So from this you can work out that pdb2gmx is guessing that residue 6 
(named "NHM" in your pdb file) is intended to be an NH2 residue (which 
has 3 atoms), but then gets confused trying to match one of them to the 
C atom in the residue named "NHM". You need to name residues according 
to the names in the .rtp database. Here, "NHM" presumably isn't right 
for N-methylamine your force field. Go and look up what it should be and 
edit your input to help pdb2gmx along.

Computers can't be programmed to guess correctly in all cases what the 
user meant. You need to take some responsibility for telling it useful 
things :-) A good working knowledge of the contents of chapter 5 of the 
manual is invaluable here.


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