From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Jan 28 2009 - 10:00:03 CST
namd assumes that any oxygen bonded to exactly two hydrogens is part of
a water molecule. Since there has been some hand-mangling of your psf,
I'd start by inspecting your molecule in vmd with the psf/pdb
combination loaded and making sure the bonding pattern is correct.
OZGE ENGIN wrote:
> I have another problem. I created the psf file of my molecule without water. Then, I tried to run it but got the following error:
> asymmetric water found??? It can not be true. I looked through the mailing list and encountered with similar problems but no satisfactory solution. What may it be due to?
> thanks in advance
> Ozge Engin
> Computational Science & Engineering
> Koc University
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