[gmx-users] Problem regarding Simulation
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
Step6: Water molecule starting at atom 5486 can not be settled.
And this error occurs severally.
Please help me.
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