[gmx-developers] Residue renaming

[hess at sbc.su.se]

>
>
> ----- 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

This was due to some issues in pdb2gmx.c.
I just committed a fix, so now everything should work,
except for using HIE as the first or last residue in th pdb input,
as discussed on gmx-users. There is an env var to automatically
treat that as well.

Berk