From: Akemi Matsuno-Yagi (ayagi_at_scripps.edu)
Date: Tue Jun 09 2009 - 15:09:25 CDT

Thanks, John, for your prompt help. That did solve my problem.
And I've learned something new with vmd.

Akemi

On 06/09/2009 12:55 PM, John Stone wrote:
> Akemi,
> Try running Extensions->Modeling->Automatic PSF Builder and
> have it generate a PSF for your structure. I think that will cure
> your problem, as it will define bonds explicitly, allowing VMD to
> skip the simplistic distance-based bond determination heuristic.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Tue, Jun 09, 2009 at 11:01:09AM -0700, Akemi Matsuno-Yagi wrote:
>> Hi,
>>
>> I have a problem that is similar to what was reported earlier:
>>
>> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/13173.html
>>
>> In my case, it is a pdb file I created using molecular modeling
>> software. It contains 2 protein subunits. Each one displays
>> without any problem. However, when the two files are combined
>> into one pdb, vmd cannot create the bonds all the way through. I
>> understand this has to do with the distance-based bond search
>> heuristic vmd employs.
>>
>> Could someone please confirm that my pdb file is suffering this
>> issue? The file is at:
>>
>> http://www.toracat.org/work/testCD.pdb
>>
>> Thank you in advance.
>>
>> Akemi
>> --
>> =========================================
>> Akemi Matsuno-Yagi, Ph.D.
>> The Scripps Research Institute
>> Dept of Molecular & Experimental Medicine
>> 10550 N. Torrey Pines Rd., MEM256
>> La Jolla, CA 92037
>> email: ayagi <at> scripps.edu
>> =========================================
>

-- 
=========================================
Akemi Matsuno-Yagi, Ph.D.
The Scripps Research Institute
Dept of Molecular & Experimental Medicine
10550 N. Torrey Pines Rd., MEM256
La Jolla, CA 92037
email: ayagi_at_scripps.edu
phone: 858-784-2596
fax  : 858-784-2054
=========================================