Re: [AMBER] sander and ptraj problem

From: manikanthan bhavaraju <manikanthanbhavaraju.gmail.com>
Date: Thu, 13 May 2010 10:42:01 -0500

Bill,
Thanks for your replies. I have few doubts regarding the current problem.
When I have analyzed the corrupted rst file, the coordinates of one water
molecule has **** in it.


Do you think that substrate de-charging process might have effected a
single water molecule?

In my case iwrap=1, was not wrapping all the water molecules around the
substrate molecule. I am using iwrap=1 option for the first time, could you
explain why it was not wrapping?

Thanks,


-- 
Manikanthan Bhavaraju
Graduate Teaching Assistant
Dept. of Chemistry
Mississippi State University
office no : 662-325-4633
MS -39762
USA.
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Received on Thu May 13 2010 - 09:00:06 PDT
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