> I was wondering if there is a way to obtain a rst file from a specific
> set of a long trajectory (ex. Obtain a rst file for set 5,345 of a
> 10,000 set binpos or crd file. I have scanned the archives and manual
> unsuccessfully for what should be a simple task. Sorry if the answer is
> already present somewhere...
You can output a set of coordinates in AMBER restart format using ptraj,
however it will not contain valid velocities (as both the crd and binpos
formats do *not* contain velocity information):
ptraj prmtop << EOF
trajin mdcrd 5345 5346 1
trajout snap5345.rst restart
EOF
Current versions of ptraj-- even if velocity information is read in (such
as with reading of restart files)-- do not output velocity information (or
more accurately stated, velocities are output as all zeros); with new
formats coming available that include velocity information, future
versions will allow creating valid restart files (subject to possible
numerical format truncation inaccuracies).
Good luck.
\-/ 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.utah.edu (801) 587-9652; FAX: (801) 585-9119
\-/ BPRP295A
http://www.chpc.utah.edu/~cheatham
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sat Jan 07 2006 - 06:10:05 PST
