On 9/20/12 4:24 AM, menica dibenedetto wrote:
Dear all,
I have a problem with pdb2gmx function.
I want to create the gro file of an acetylated at N-term protein.
I copy here the head of the file:
ATOM 2016 HC ACE 0 24.770 -62.381 -11.080 H
ATOM 2015 CT ACE 0 25.644 -61.867 -10.739 C
ATOM 2017 HC ACE 0 26.283 -61.657 -11.571 H
ATOM 2018 HC ACE 0 26.167 -62.480 -10.034 H
ATOM 2013 C ACE 0 25.231 -60.546 -10.063 C
ATOM 2014 O ACE 0 24.058 -60.199 -9.966 O
TER
ATOM 2019 N MET 1 26.336 -59.728 -9.542 N
ATOM 2020 H MET 1 27.236 -59.762 -9.976 H
ATOM 1 CA MET 1 26.144 -59.704 -8.063 C
The problem is that the output error told me that the atoms labels of
ACE not correspond to the labels in the rtp file,
but I checked it and them corresponds:
Program pdb2gmx_d, VERSION 4.5.5
Source code file: pdb2gmx.c, line: 655
Fatal error:
Atom HC in residue ACE 0 was not found in rtp entry ACE with 6 atoms
while sorting atoms.
I used the amber99sb-ildn.ff
What can I do?
You've confused atom name with atom type. Refer to the aminoacids.rtp file for
the force field. I would also suggest removing the "TER" from between the ACE
and MET, otherwise pdb2gmx is likely going to try to write them as separate chains.
-Justin
--
========================================
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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