[gmx-developers] Residue renaming

[Mark Abraham]

----- 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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