AMBER Archive (2002)

Subject: Re: "crd" file created with VMD

From: Soonmin Jang (sjang_at_protege.snu.ac.kr)
Date: Wed Jul 24 2002 - 02:28:27 CDT

Yes,
I figured out the same way and I made small program that can convert this
trajectory file into restart file(coordinate only of course).
Now it works.
Thank you.

Soonmin
>
> 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
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> ==================================================================
>