Re: asymmetric water found!

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Jan 28 2009 - 10:00:03 CST

Hi Ozge,
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.
Peter

OZGE ENGIN wrote:
> Hi,
>
> 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

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:50:27 CST