[gmx-users] problem with phosphorylated serine

[Jayant James]

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"
Thanks!
JJ
PS.

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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