AMBER Archive (2006)

Subject: Re: AMBER: ptraj and mdvel question

From: Thomas Cheatham (tec3_at_utah.edu)
Date: Wed Nov 15 2006 - 17:37:13 CST

> In ptraj, I can use "trajin mdcrd 1 n 1" to read in the trajectory
> coordinate file. Can I also put in the mdvel file at the same time and
> then save output file about the coordinate and velocity to pdb format?

I never tried this until just a minute ago, but since the mdcrd and mdvel
files have the same format, ptraj handles it just fine treating the x, y,
z velocities as if they were coordinates. You cannot do both
simultaneously (i.e. the PDB format only has positions for three
coordinates, replaced with velocities if you read a mdvel file). There is
no way to read both (and create a restrt file with coordinates and
velocities) at present, although this may be useful (except noting of
course that the low precision of the dumped velocities may not be all that
helpful/accurate).

If you really want accurate coordinates and velocities, the NetCDF
trajectory file (supported in AMBER 9) is the best way to go, but at
present I think ptraj only writes out coordinates (ignores velocities on
writing) at present.

--tom

\-/ 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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