[gmx-users] Regarding errors

Seera Suryanarayana palusoori at gmail.com
Mon May 14 11:28:23 CEST 2012

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,

                                  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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