[gmx-users] problem pdb2gmx and acetylation
domenica.dibenedetto at gmail.com
Thu Sep 20 11:46:39 CEST 2012
Thanks!! :) now works!
2012/9/20 Justin Lemkul <jalemkul at vt.edu>:
> 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
>> ATOM 2015 CT ACE 0 25.644 -61.867 -10.739
>> ATOM 2017 HC ACE 0 26.283 -61.657 -11.571
>> ATOM 2018 HC ACE 0 26.167 -62.480 -10.034
>> ATOM 2013 C ACE 0 25.231 -60.546 -10.063
>> ATOM 2014 O ACE 0 24.058 -60.199 -9.966
>> ATOM 2019 N MET 1 26.336 -59.728 -9.542
>> ATOM 2020 H MET 1 27.236 -59.762 -9.976
>> ATOM 1 CA MET 1 26.144 -59.704 -8.063
>> 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 A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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