AMBER Archive (2002)

Subject: Re: "crd" file created with VMD

From: David Case (case_at_scripps.edu)
Date: Wed Jul 24 2002 - 02:04:02 CDT

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 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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