AMBER Archive (2006)

Subject: AMBER: RE: trouble stripping waters with ptraj

From: Adam Pelzer (yankeeswin314159_at_yahoo.com)
Date: Mon May 29 2006 - 17:20:23 CDT

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
also create an average structure,

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:
> rms reference mass out no_salt_prod_avrg_pdb_all.rms time 2 @1-5783 name no_salt_prod_avrg_pdb_all_rms
> rms reference mass out no_salt_prod_avrg_pdb_2.rms time 2 :30-66 name no_salt_prod_avrg_pdb_2_rms

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 .................................................
> Set 250
> ERROR in readAmberTrajectory(): Set #251 is corrupted (
> �����?�y% ��l?qO÷¼ ¿7)...

As professor Simmerling mentioned, it looks like the terminal was reset.
I am working to fix that warning message behavior to prevent the
confusion...

Check out the produced RMSd files to see if this makes sense. You could
also create an average structure,

average avg.pdb pdb

and look at this...

\-/ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy
-/- Departments of Med. Chem. and of Pharmaceutics and Pharm. Chem.
/-\ Adjunct Asst Prof of Bioeng.; Center for High Performance Computing
\-/ University of Utah, 30 S 2000 E, SH 201, Salt Lake City, UT 84112
-/-
/-\ tec3_at_utah.edu (801) 587-9652; FAX: (801) 585-9119
\-/ BPRP295A http://www.chpc.utah.edu/~cheatham

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