VMD-L Mailing List

From: Mark Zottola - Contractor (mzottola_at_arl.army.mil)
Date: Wed Nov 13 2002 - 16:04:39 CST

My crd file is 10 columns wide but there are no %FLAG keywords scattered in
the topology file.

And much as I hate to admit it, I am running the Windows version 1.8a29 of
VMD.

Thanks!
*****************************************************************
Dr. Mark A. Zottola
PET Director of Computational Chemistry and Materials
Army Research Laboratory MSRC
PB 191 939-I Beards Hill Road
Aberdeen MD 21001
VOICE: 410 278 7250 FAX: 410 297 9521

                                                                                                                                     
                      "B. Bennion"
                      <bbennion_at_u.washington. To: Mark Zottola - Contractor <mzottola_at_ARL.ARMY.MIL>
                      edu> cc: vmd-l_at_ks.uiuc.edu
                                               Subject: Re: CRD problems and CRD to DCD conversion
                      11/13/02 04:48 PM
                                                                                                                                     
                                                                                                                                     
                                                                                                                                     

Hi Mark,

Are your crd files ten columns wide or six? Restart crds are 6 columns
and normal crds are ten columns in amber 7 output. Also does you prm/top
file
have %FLAG keywords scattered throughout?

if you have linux version of vmd continue reading;
There are beta plugins for amber 7 prm/top files that can be downloaded
with the linux? binaries. There is also a restart plugin for amber 7
restart crd files that can be downloaded from the same place. Otherwise
the normal crd plugin will read the 10 column crd file once the prm file
has been read in correctly.

On Wed, 13 Nov 2002, Mark Zottola - Contractor wrote:

> Date: Wed, 13 Nov 2002 15:59:33 -0500
> From: Mark Zottola - Contractor <mzottola_at_arl.army.mil>
> To: vmd-l_at_ks.uiuc.edu
> Subject: CRD problems and CRD to DCD conversion
>
> I am trying to use VMD for a visualization project here. I am using
AMBER
> to generate a dynamics trajectory. AMBER produces a .crd file containing
> the coordinates of the system at each time step sampled (sampling every
25
> fs on a rather long simulation). It turns out that VMD will not read the
> file because AMBER's idea of crd and VMD's idea of crd are two different
> things.
>
> Now I would LIKE to visualize the trajectory using VMD. Is there any way
I
> can massage my CRD file to make it readable to VMD or is there a
relatively
> easily obtained CRD to DCD converter out there?
>
> This is, unfortunately a "time is of the essence" request, so quick
replies
> are deeply appreciated.
> *****************************************************************
> Dr. Mark A. Zottola
> PET Director of Computational Chemistry and Materials
> Army Research Laboratory MSRC
> PB 191 939-I Beards Hill Road
> Aberdeen MD 21001
> VOICE: 410 278 7250 FAX: 410 297 9521
>
>

Graduate Research Assistant
Dep. Medicinal Chemistry, University of Washington
Tel# (206)616-2779
BOX 357610 Seattle WA 98195

email--bbennion_at_u.washington.edu
web page--http://students.washington.edu/bbennion