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

Abil Aliev abil4616 at yahoo.co.uk
Wed Dec 15 17:44:33 CET 2004

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.

> 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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