[gmx-users] methanol/water mixture with all atoms

Yousung Jung yousung at gmail.com
Wed Mar 1 07:54:54 CET 2006

(1) I downloaded equilibrated methanol box (pdb) with opls from the gromacs
website (I need an all-atom model for MeOH).  When I pdb2gmx, I get the
following error message:

Fatal error:
Atom HB in residue MET 1 not found in rtp entry with 17 atoms
             while sorting atoms. Maybe different protonation state.
             Remove this hydrogen or choose a different protonation state.
             Option -ignh will ignore all hydrogens in the input.

Whate would be the source of problem?

(2) What I really want is an all-atom butanol/water or methanol/water (1:3
in mole fraction) mixture with about 400 molecules total. How do people
usually generate initial coordinate file for such a system? I just started
to run MD simulation, so any know-hows would be greatly appreciated.

(3) Does opls/tip4p sound like a reasonable combination for the simulation
of the methanol/water system? If not, could you please recommend one?

Thanks very much!
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