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