[gmx-users] problem pdb2gmx and acetylation

[menica dibenedetto]

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
>> 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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