AMBER Archive (2006)

Subject: Re: [UCE]AMBER: RE: trouble stripping waters with ptraj

From: Thomas Cheatham (
Date: Fri May 26 2006 - 11:04:22 CDT

> 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

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
/-\ (801) 587-9652; FAX: (801) 585-9119
\-/ BPRP295A

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