[gmx-users] Water molecule near protein surface cannot be settled.

[Dawid das]

Dear Gromacs experts,

I have encountered quite annoying problem again. When I try either
minimization or NVT dynamics of my solvated protein system I get message
like this:

step -1: Water molecule starting at atom 16281 can not be settled.

It is for couple of water molecules. I have checked visually where these
molecules are and for minimization they are near surface of protein (not
buried inside). I attach the link for *gro, *top, *log and other files.
What can I do about it?

http://www.speedyshare.com/rN4gx/mCherry7-min.tar.bz2
http://www.speedyshare.com/BnwU5/mCherry7-nvt-md.tar.bz2
http://www.speedyshare.com/3k9jz/charmm27-files.tar.bz2

Best wishes,

Dawid Grabarek