From: bora erdemli (boraerdemli_at_yahoo.com)
Date: Wed Dec 22 2004 - 02:26:19 CST
When you neutralize your protein, the plug in puts the
ions 5 Angstrom apart from the nearest atom as
default. If you change the distance to the larger
value it may solve your problem? It is just a
suggestion, it is kind of difucult to say something
without looking at your input file. However, at least
you can try it.
--- Gaurav Sharma <sharma_at_coe.neu.edu> wrote:
> Hi All,
> I am getting the following error while running my
> simulation of a protein solvated in a water box
> using periodic boundary conds.
> FATAL ERROR: Asymmetric water molecule found??? This
> can't be right.
> I first solvated the protein and then neutralized
> the charge on the whole system by using autoionize
> plugin. It placed 17 CLA ions in the system. While
> running the simulation I get the above error. I have
> attached a part of the output log file for your
> Thanks in advance for your help.
> Gaurav Sharma
> Computational BioNano Robotics Lab
> Northeastern University
> Boston, MA - 02115
> Tel: 617-373-2970
> ATTACHMENT part 2 application/octet-stream
Sabri Bora Erdemli
Computational Science and Engineering
Research and Teaching Asistant
Koc Universitesi pk.218 34550
tel no: 02123381736
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