[gmx-developers] Residue renaming

Alexey Shvetsov alexxyum at gmail.com
Wed Aug 25 14:05:39 CEST 2010

Actualy input file is speptide.pdb froms share/tutor/speptide
It has residue name as HIS. To reproduce this error simpy run pdb2gmx
with this file and select amber99-idln ff

2010/8/25 Mark Abraham <mark.abraham at anu.edu.au>:
> ----- Original Message -----
> From: Alexey Shvetsov <alexxyum at gmail.com>
> Date: Wednesday, August 25, 2010 20:18
> Subject: [gmx-developers] Residue renaming
> To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
>> Hi all!
>> Seems pdb2gmx started renaming HIS residues to HISE HISD and
>> HISH. So
>> in latest build with amberff  i started getting this
>> -------------------------------------------------------
>> Program pdb2gmx, VERSION 4.5-beta3-20100825-ea694aa-dirty
>> Source code file: ../../../gromacs-4.5.9999/src/kernel/resall.c,
>> line: 552
>> Fatal error:
>> Residue 'HISE' not found in residue topology database
>> For more information and tips for troubleshooting, please check
>> the GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> -------------------------------------------------------
> What's the problem? If your input file uses HISE, then you'll need to adapt
> to the fact that the AMBER .rtp files all use HID/HIP/HIE. Unfortunately
> there are no standard naming treatments for the histidine variants.
> Mark
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Best Regards,
Alexey 'Alexxy' Shvetsov
Petersburg Nuclear Physics Institute, Russia
Department of Molecular and Radiation Biophysics
Gentoo Team Ru
Gentoo Linux Dev
mailto:alexxyum at gmail.com
mailto:alexxy at gentoo.org
mailto:alexxy at omrb.pnpi.spb.ru

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