VMD-L Mailing List

From: Margaret Cheung (cheung_at_physics.ucsd.edu)
Date: Thu Oct 24 2002 - 15:57:50 CDT

Hi, Vlad,

It may be very likely that format of your CRD files need to be modified.
For VMD, it reads only "one" blank card in the mdcrd file.
Please check the first two lines of your mdcrd file. Make sure
that the coordiates starts at the second line.

Sincerely,
Margaret S. Cheung
Physics Department 0319
University of California, San Diego
9500 Gilman Drive,
La Jolla, CA 92093-0319
http://www-physics.ucsd.edu/~cheung

On Thu, 24 Oct 2002, Vlad Cojocaru wrote:

> Dear AMBER and VMD users,
> I am trying to visualize a AMBER trajectory made with carnal using vmd
> If I take each trajectory and unzip as it was row created by AMBER
> everything is fine but if I load into vmd the trajectory outputed by
> carnal it loads something really strange. Could somebody tell why this
> behaviour?
> The input files for CARNAL are:
>
>
> FILES_IN
> PARM p1 ../../rna_ion_wat.top;
> STREAM s1 ../../rna_ion_wat_mdeq_final.mdcrd.gz;
> FILES_OUT
> COORD crd movie.mdcrd;
> DECLARE
> GROUP g1 (RES 1-17);
> IMAGE img g1%cmass;
> OUTPUT
> COORD crd s1 MOD 10;
> END
>
> and:
>
> FILES_IN
> PARM p1 ../../rna_ion_wat.top;
> STREAM s1 ../../rna_ion_wat_mdprd00.mdcrd.gz
> ../../rna_ion_wat_mdprd01.mdcrd.gz
> ../../rna_ion_wat_mdprd02.mdcrd.gz
> ../../rna_ion_wat_mdprd03.mdcrd.gz
> ../../rna_ion_wat_mdprd04.mdcrd.gz
> ../../rna_ion_wat_mdprd05.mdcrd.gz
> ../../rna_ion_wat_mdprd06.mdcrd.gz;
> FILES_OUT
> COORD crd movie.mdcrd APPEND;
> DECLARE
> GROUP g1 (RES 1-17);
> IMAGE img g1%cmass;
> OUTPUT
> COORD crd s1 MOD 50;
> END
>
> Is there another way to select certain frames from a suite of
> trajectories???
> Thanks a lot for any replies!
> Best wishes,
> vlad
>
> --
> Vlad Cojocaru
> Max Planck Institut for Biophysical Chemistry
> Deparment: 060
> Am Fassberg 11, 37077 Goettingen, Germany
> tel: ++49-551-201.1389
> e-mail: Vlad.Cojocaru_at_mpi-bpc.mpg.de
>
>
>
>