VMD-L Mailing List

From: Jennie Thomas (jenniet_at_uci.edu)
Date: Tue Nov 21 2006 - 14:46:10 CST

John,

I'm sorry, after looking more carefully I see that vmd is not writing
the box information just for the first step. I made the mistake of
thinking that the box information was not correct for the other steps
in the Amber coordinate file I'm writing because the first step
listed 0.0 0.0 0.0 as the box dimensions. This is not a problem with
VMD, but with the data I loaded. There must not be box information
in my .cor file (which is used only for the first step). I'll just
modify my .tcl script to write everything but the first step and I
should have box information I need.

Thanks so much for your help!

Cheers,
Jennie

On Nov 21, 2006, at 11:22 AM, John Stone wrote:

>
> Jennie,
> Hmm, can you show me the exact commands you're using when you
> write the CRD? It worked for me when I did this simple test:
> mol new 1e79
> molinfo top get { a b c }
> (output is "267.200012 107.199997 135.899994")
>
> # write the CRD file with box info
> set sel [atomselect top all]
> $sel writecrdbox foo.crd
>
> # last line of the CRD is the box size (for 1e79):
> tail -1 foo.crd
> (output is " 267.200 107.200 135.900")
>
> Let me know if this helps clarify things.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
>
> On Tue, Nov 21, 2006 at 11:13:46AM -0800, Jennie Thomas wrote:
>> 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
>>>
>
> --
> 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
>