[gmx-users] Problem regarding Simulation

madhumita das madhumita.bioinfo at gmail.com
Wed Nov 2 12:04:42 CET 2011

Hi GROMACS users,

            I have generated .prmtop and .inpcrd files using xleap module
of AMBER for a  single chain of a membrane protein molecule containing a
modified residue. After that I have converted those files into .gro,.top
,em.mdp and md.mdp files with the help of acpype.py. But using the md.mdp
file for simulating that protein in waterbox without membrane produces
following error:

  Step6: Water molecule starting at atom 5486 can not be settled.

And this error occurs severally.

                                 Please help me.

Yours faithfully,

Madhumita Das
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