AMBER Archive (2006)

Subject: Re: AMBER: creating a RST file from specific set of binpos/crd file

From: Thomas E. Cheatham, III (
Date: Fri Jan 06 2006 - 11:53:51 CST

> 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

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

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