[gmx-users] pdb2gmx -ff oplsaa -water tip4p / cut-offs for oplsa
abil4616 at yahoo.co.uk
Wed Dec 15 19:08:00 CET 2004
hmm, i thought smileys were not so cool... but thanks, i have my answer.
>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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