VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Mon Mar 20 2006 - 13:09:04 CST

Hi Brian,
I think this may be due to some disagreement between nomenclature in
some pdb files and some topology files. I'm looking into it.
Thanks,
Peter

Brian Bennion wrote:

> Hi Peter
>
> After I sent the first email regarding autopsf, (apologies to those
> email clients that choked on a 1.4M attachment), I ran the same pdb
> file through my standalone psfgen that came with vmd1.8.3 and still
> saw the same problem.
>
>
> brian
>
>
> On Sun, 19 Mar 2006, Peter Freddolino wrote:
>
>> Hi Brian,
>> could you please send me the topology file and script you used to run
>> the psfgen standalone on this structure? I am able to reproduce this
>> error, so if you send me the rest of that data I should be able to
>> fix it.
>> Many thanks,
>> Peter
>>
>> Brian Bennion wrote:
>>
>>>
>>> Hello,
>>>
>>> I have been testing the new features in 1.8.4b11 (sorry I know I am
>>> one behind) for windows and noticed that placement of hydrogens on
>>> the branching Carbon of Leucine sidechains is placed parallel to the
>>> axis of the Cbeta-Cgamma carbon bond.
>>> ie
>>> CH3
>>> /
>>> Ca-Cb-HCg
>>> \
>>> CH3
>>>
>>> instead of something more reasonable like...
>>>
>>> CH3
>>> /
>>> Ca-Cb-Cg-H
>>> \
>>> CH3
>>>
>>>
>>> Attached are the before and after pdb files. If these hydrogen
>>> placements are left in the current position the miniziation will fix
>>> them but often requires MAJOR side motions...
>>>
>>> I haven't seen this behavior in older standalone psfgen use.
>>>
>>> Brian
>>>
>>>
>>> ************************************************
>>> Brian Bennion, Ph.D.
>>> Biosciences Directorate
>>> Lawrence Livermore National Laboratory
>>> P.O. Box 808, L-448 bennion1_at_llnl.gov
>>> 7000 East Avenue phone: (925) 422-5722
>>> Livermore, CA 94550 fax: (925) 424-6605
>>> ************************************************
>>
>>
>
> ************************************************
> Brian Bennion, Ph.D.
> Biosciences Directorate
> Lawrence Livermore National Laboratory
> P.O. Box 808, L-448 bennion1_at_llnl.gov
> 7000 East Avenue phone: (925) 422-5722
> Livermore, CA 94550 fax: (925) 424-6605
> ************************************************