[gmx-users] pdb2gmx -ff oplsaa -water tip4p / cut-offs for oplsa

David spoel at xray.bmc.uu.se
Wed Dec 15 18:23:17 CET 2004

On Wed, 2004-12-15 at 16:44 +0000, Abil Aliev wrote:
> thanks, David. what about 2 different types of tip4p:
> "pdb2gmx -ff oplsaa -water tip4p" results in HO4 with HW1 for 
> crystallographic water, whereas "genbox -cs tip4p" gives MW1 for the 
> added water molecules (the other 3 atoms are the same). in fact, without 
> manually editing the gro file grompp simply fails, complaining about 
> different number of atoms in top and gro files.
Since you have discovered this, you can probably fix it too :).

Some MD equilibration will fix all your problems in this respect.
> > with the above i get OW1,HW1,HW2 and HW4 for crystallogrphic waters 
> > which are labelled as HO4. after editconf/genbox -cs tip4p i get a 
> > different type for added water with HW1 above replaced by MW1. i can 
> > change HW1 to MW1 and HO4 to HOH before genbox to get the grompp 
> > working, but is this the right way to proceed?
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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