Re: namd: adding water molecules

From: Sergio Anis (
Date: Thu May 11 2006 - 21:52:18 CDT

hi Elsa;

i had the rigidBonds set to all, so setting it to none it run without

i have two extra concerns:
* how this setting will affect my simulation (compare to setting
rigidBonds to all)
* i have to compare this simulation (with water inside the active site)
vs others (without water, with substrate)that i already run. Do you
think i'd run them again using rigidBonds none, or i can still compare them?

thanks again;

PS: hi Michel; the active site is close to the surface and i checked the
distances and only one of the oxygen is 2.48 A from the protein (the
rest is 2.92 and up). So, i don't think that it is the problem. Thanks
for answering

good night,


Elsa F. Sousa Henriques wrote:
> Have you set 'rigidBonds' to all or water? If so, as a simple test, try
> to run a few simulation steps with rigidBonds set to none ... it may
> just be that psfgen made a poor initial guess of the hydrogen atoms of
> your "buried" waters and ShakeH is unable to resolve it.
> Hope it helps,
> Elsa
> Quoting Sergio Anis <>:
>> hi everybody,
>> i'm having some problems when i try to add water molecules to my system
>> i need to add some water molecules inside the protein (in the active
>> site), so i put oxygen atoms (classified as OH2, residue TIP3) and let
>> the guesscoord to add the H
>> when i run simulation i receive the error message: 'asymmetric water
>> molecule found' and the simulation crash
>> what does this mean?, and why this doesn't happen when the TIP3 water
>> molecules are outside the protein (forming the water box)?
>> i appreciate any help on this
>> thanks
>> sergio

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