[gmx-users] Regarding errors

Anik Sen aniksen at csmcri.org
Mon May 14 11:57:21 CEST 2012

Dear Suryanarayana Seera

    Please check the itp files mentioned in the topol.top and what u used in your commands. Especially check the solvent model. May be you have not changed that in the topol.top file.
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Seera Suryanarayana [palusoori at gmail.com]
Sent: Monday, May 14, 2012 2:58 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] Regarding errors

Dear all gromacs users,

    I tried the grompp and i got the following error."number of coordinates in coordinate file (4INS_b4ion.gro, 90396)
                                  does not match topology (4INS.top, 90393)".

                                  Is there any explanation why is this happens.I would appreceate any help.I am new in using moleculer dynamics and particularly in gromacs.

Atom HA in residue MET 1 was not found in rtp entry MET with 11 atoms
while sorting atoms.

For a hydrogen, this can be a different protonation state, or it
might have had a different number in the PDB file and was rebuilt
(it might for instance have been H3, and we only expected H1 & H2).
Note that hydrogens might have been added to the entry for the N-terminus.
Remove this hydrogen or choose a different protonation state to solve it.
Option -ignh will ignore all hydrogens in the input.

Suryanarayana Seera,
PhD student,
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