On Wed, Jul 24, 2002, Soonmin Jang wrote:
> Here is more info about 'crd' file I created with VMD.
>
> cqd1[vii] 1> head a.crd
> TITLE
> 36.039 65.537 -11.797 36.952 66.130 -11.743 36.802 67.111 -12.193 37.633
> 65.521 -12.337 37.339 66.272 -10.250 36.806 65.488 -9.442 38.257 67.190
I think it's just a matter of terminology. What you and VMD call call
a 'crd' file is also called a "trajectory file" in Amber (although Amber
also calls it "mdcrd", so the VMD nomenclature makes sense.)
What you need for the -c option of sander is a "restart file", which (in
Amber) is generally created either by saveAmberParm in LEaP, or through
the -r option in sander.
This file is only trivially different from a one-frame "trajectory file", so
you could convert via a small script. Or, maybe VMD has a way of creating
what you need directly.
[In more detail: a "trajectory file" can have multiple coordinate sets. A
"restart file" has just one set of coordinates, but it may also have
velocities. Both formats can optionally record box-size information as
well.]
...good luck...dac
--
==================================================================
David A. Case | e-mail: case_at_scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
==================================================================
Received on Wed Jul 24 2002 - 00:04:02 PDT
