Re: HSE and gromacs

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Sun Feb 10 2008 - 10:49:46 CST

Erm, excuse me, I mean "make an index file with an entry for 'protein or
resname HSE'"
Peter

Peter Freddolino wrote:
> sed s/HSE/HIS/g namd_pdbfile > gromacs_pdbfile
>
> Or, use gromacs' make_ndx program to make an index file with an entry
> for protein or resname HIS, and use this ndx file in all of your
> analysis.
>
> Peter
>
> patrick wintrode wrote:
>> Hi,
>>
>> I've noticed that when I calculate RMSFs for my trajectory using
>> gromacs, it treats all of the histidines as non-protein elements,
>> presumably because they are labeled HSE rather than HIS.
>>
>> Do I need to alias my entire trajectory back to HIS? If so, can
>> someone suggest the easiest way to do this?
>>
>> Thanks.
>>
>> Patrick L. Wintrode
>> Department of Physiology & Biophysics
>> Case Western Reserve University
>> Cleveland, OH 44106

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