VMD-L Mailing List

From: Jennie Thomas (jenniet_at_uci.edu)
Date: Tue Nov 21 2006 - 13:13:46 CST

Hello John,

Thanks for your help with this. I'm using VMD for MACOSXX86, version
1.8.5 (August 25, 2006). I would be happy to send you an example
script and also the trajectory I'm using if you would like to do a test.

When I load the dcd trajectory in vmd, I can get the box information
at every timestep by simply changing the frame and using:

atomselect top get a
atomselect top get b
atomselect top get c

So, there is no doubt that vmd has the box information at every
timestep loaded correctly. However, the box information is missing
when I write the .crd file. Instead of getting the actual box
information I get 0.0 0.0 0.0 in place of the box dimensions. This
is a cubic box, so I don't need alpha, beta, and gamma.

Thanks!
Jennie

On Nov 21, 2006, at 9:21 AM, John Stone wrote:

> Hi,
> I just checked the current versions of VMD and the AMBER CRD plugin,
> and they already support writing of box information. The CRD format
> only stores the a/b/c side lengths however, and not the alpha/beta/
> gamma
> angles, so the conversion from DCD to CRD will lose that information.
> Which version of VMD were you using for your tests?
>
> Thanks,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Mon, Nov 20, 2006 at 10:46:26PM -0600, John Stone wrote:
>>
>> Jennie,
>> I'll have to take a look at the AMBER CRD plugin tomorrow and
>> see if the
>> problem is simply that it doesn't include code to write the box
>> information. If so, it may be a simple matter to add and send you a
>> new version of the AMBER CRD plugin to try out.
>>
>> John Stone
>> vmd_at_ks.uiuc.edu
>>
>> On Mon, Nov 20, 2006 at 08:09:12PM -0800, Jennie Thomas wrote:
>>> Hi VMD experts,
>>>
>>> I have an analysis code (separate from VMD) that reads in AMBER
>>> coordinate files. Someone has asked if I can use this code to
>>> analyze a dcd trajectory, so I decided to try and use vmd to convert
>>> from dcd to crdbox format. However, the box information is not
>>> preserved when doing this. Because this is a constant pressure
>>> simulation I need to use the box information at every step. Do you
>>> know how to force vmd to write box information?
>>>
>>> I have a simple tcl script I am using:
>>>
>>> # Load the system and the trajectory
>>> mol new "box.cor" type cor
>>>
>>> mol addfile "00.trj" type dcd waitfor all
>>> mol addfile "01.trj" type dcd waitfor all
>>>
>>> animate write crdbox traj.crd
>>>
>>> Do I need to be doing something more complicated to get box
>>> information? Or does anyone have another suggestion for a file
>>> format conversion tool?
>>>
>>> Thanks,
>>> Jennie Thomas
>>
>> --
>> NIH Resource for Macromolecular Modeling and Bioinformatics
>> Beckman Institute for Advanced Science and Technology
>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
>> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>