|
|||||||||||||||||||||||||||||||||
AMBER Archive (2006)Subject: AMBER: RE: trouble stripping waters with ptraj
From: Adam Pelzer (yankeeswin314159_at_yahoo.com)
Dr. Cheatham:
Thank you very much for your reply. I have one question about your suggestions. You wrote:
Check out the produced RMSd files to see if this makes sense. You could
average avg.pdb pdb
and look at this...
I looked at the produced RMSd files and they seem fine, but I'm not sure what you mean when you suggest that I create an average structure. What trajectory would I be averaging, and what would I be looking for in order to confirm the validity of the RMSd files that were produced? If you could please clarify what you meant, I would be very grateful.
Thank you for all of your advice.
Adam
Thomas Cheatham <tec3_at_utah.edu> wrote:
Were these output files produced and do they look reasonable when plotted?
> File (no_salt_prod_water_stripped.mdcrd) is an AMBER trajectory with 250 sets
250 sets/frames were found; hopefully this is what you expected.
> Set 200 .................................................
As professor Simmerling mentioned, it looks like the terminal was reset.
Check out the produced RMSd files to see if this makes sense. You could
average avg.pdb pdb
and look at this...
\-/ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy
__________________________________________________
| |||||||||||||||||||||||||||||||||
|