AMBER Archive (2002)

Subject: Re: ptraj problem

From: Prabal Maiti (maiti_at_wag.caltech.edu)
Date: Tue May 21 2002 - 18:51:22 CDT

There are two things:
When you want to get the average str you need to specify the format
(either pdb or restart).
average dna-avg.crd pdb(or restart).
To calculate the rms w.r.t to the average str. you need to first get it by
ptraj and then you have to run ptraj again with that average str. to get
rms.
I am not sure if ptraj can output multiple things, like first generate
average str. and then use it and get rms at the same time. For me atleast
it didnt work.
Hope this helps
Prabal

On Tue, 21 May 2002, Jake Isaacs wrote:

>
> I can't seem to get ptraj to output rms values from a trajectory. Here is
> my input script:
>
> trajin dna1001-2000.crd 1001 2000 1
> average dna-avg.crd
> reference dna-avg.crd
> rms reference mass out dna-rms.out
> trajout dna1001-2000-rms.crd
> go
>
> The problem is that dna-rms.out never gets created, much less written to.
>
> .-. .-. .-. .-. .------------------------. .-. .-. .-. .-.
> /|||X|||\ /|||X|||\ / Richard J. (Jake) Isaacs \ /|||X|||\ /|||X|||\
> X|||/ \|||X|||/ \|||X Department of Molecular X|||/ \|||X|||/ \|||X
> `-' `-' `-' `-' \ & Cellular Biochemistry / `-' `-' `-' `-'
> .-. .-. .-. .-. / University of Kentucky \ .-. .-. .-. .-.
> X|||\ /|||X|||\ /|||X 800 Rose St. X|||\ /|||X|||\ /|||X
> \|||X|||/ \|||X|||/ \ Lexington, KY 40536-0084 / \|||X|||/ \|||X|||/
> `-' `-' `-' `-' `------------------------' `-' `-' `-' `-'
> 

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Prabal K Maiti                             Email:maiti_at_wag.caltech.edu
Beckman Institute (139-74)                       pkmaiti_at_yahoo.com
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