VMD-L Mailing List

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Mon Mar 20 2006 - 10:27:52 CST

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
************************************************