[gmx-users] problem pdb2gmx and acetylation

[Justin Lemkul]

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

-- 
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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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