VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Mon Mar 20 2006 - 17:00:30 CST

I should clarify exactly what I mean by nomenclature. The CD1 and CD2
atoms of leucine are chemically equivalent; however, they are spatially
non-equivalent (when CD1 and CD2 are distinguishable, CG becomes a
chiral center), and if you're going to use one of them to assign the
location of HG, you have to know their relative orientations. PDB files
from the actual PDB seem to be laid out (I couldn't find this anywhere
official) such that if you look down the axis of the CG-HG bond, with
the CG-CB bond pointed down, then CD1 is to your left and CD2 is on your
right. However, the internal coordinates provided in charmm topology
files from version <= 27 expect the reverse of this, and thus build the
location of HG while looking at the position of the wrong delta carbon
(this is why the bond tilts to be almost on top of the CB-CG bond).
Does this make more sense?
Peter

Brian Bennion wrote:

> 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
> ************************************************