VMD-L Mailing List

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Mon Mar 20 2006 - 16:54:20 CST

Hi Peter,

Thank you for your work on this. I downloaded the pdb file (2blx) from
www.pdb.org and double checked the nomenclature of this particular atom
against my charm27 topology files. I didn't see a difference in the CG
nomenclature, so am I missing the whole point here?

Brian

On Mon, 20 Mar 2006, Peter Freddolino wrote:

> Hi Brian,
> this turns out to actually be a fairly common problem that people encounter
> with some topology files. Until version 31 of the charmm topology files,
> charmm and the PDB maintained a different nomenclature for the leucine delta
> carbons; as a result, hydrogens would be placed in the wrong place. There is
> really no standard for how this assignment is done, so depending on where you
> got your pdb file from you'd need different topology files or aliases to have
> things work correctly; a lot of people have used different fixes for this.
> Unfortunately, I didn't set up the right aliases in autopsf; this will be
> fixed in the next version. In general, if you're dealing with a topology file
> that doesn't give you the right leucine HG position, you can fix it by either
> using the aliases
> pdbalias atom CD1 CD2
> pdbalias atom CD2 CD1
>
> or by deleting the line
> IC CD1 CD2 *CG HG 1.5361 110.2600 -116.6300 108.0200 1.1168
> from the LEU entry of your topology file, which will cause psfgen to guess
> the position of this atom (which it will correctly place).
>
> I should stress that the former of those two solutions should work right for
> most RCSB-derived PDBs but is incompatible with the charmm nomenclature; the
> latter solution should work for all cases (although the H-C bond distance
> will be slightly off because you're not using the distance provided in the IC
> entry; this shouldn't be much of a problem because it will just default to a
> 1.0 angstrom bond instead of 1.12).
>
> To help people notice problems of this type, psfgen will give warnings and
> automatically guess coordinates of this type where the coordinate generation
> results in bad contacts. This really seems to fall into that category of
> problems with computers doing exactly what their input tells them to.
>
> I hope this is helpful please let me know if you have any further questions.
> Best,
> 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
>> ************************************************
>

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