[gmx-users] problem with phosphorylated serine

Jayant James jayant.james at gmail.com
Mon Nov 17 02:26:11 CET 2014

Hi !
I downloaded the ffG43a1p.tar.gz
<http://www.gromacs.org/@api/deki/files/12/=ffG43a1p.tar.gz> for
simulations of phosphorylated serines (downloaded from
http://www.gromacs.org/Downloads/User_contributions/Force_fields). Upon
running the pdb2gmx command in gromacs version VERSION 4.5.4. I get this
error (below). Well there is no "HISE" in the input pdb file. There is a
SEP. So I thought I'd better get help from the GMX community. I also found
that if I were to execute a pdb file without any phosphorylated serine the
pdb2gmx runs all the way to the end and the gives the error message similar
to one below.

Error message

"Program pdb2gmx, VERSION 4.5.4
Source code file: resall.c, line: 581
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"

I execute a modular command to enable execution of GMX from my directory
the commands are below
setenv         GROMACSHOME /share/apps/gromacs/4.5.4/single
prepend-path     PATH /share/apps/gromacs/4.5.4/single/bin
prepend-path     LD_LIBRARY_PATH /share/apps/gromacs/4.5.4/single/lib
prepend-path     MANPATH /share/apps/gromacs/4.5.4/single/man


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