Re: HSE and gromacs

From: Peter Freddolino (
Date: Sun Feb 10 2008 - 10:47:19 CST

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.


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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