Re: namd: adding water molecules

From: L. Michel Espinoza-Fonseca (
Date: Thu May 11 2006 - 01:34:12 CDT


Most probably this water molecule is also bound to something else.
What's the the minimal distance between the Oxygen and your protein?
Is the active site hidden in a deep cavity or close to the surface?
Did you try to solvate the protein using VMD?

My suggestion is to put your water molecules within the active site
using a distance of ~2.5 A from the protein. This will help psfgen to
make better coordinate guesses.

Hope it helps,


2006/5/11, 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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