VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Jan 29 2010 - 09:18:32 CST

On Thu, 2010-01-28 at 17:32 -0600, snoze pa wrote:
> Dear VMD users,
>
> I am trying to calculate the Hbond formation in one of the NAMD
> tutorials. I use both VMD and chimera and obtained different results
> about Hbonds. A snapshot of the both is available at
> http://img191.imageshack.us/img191/9084/screenshotva.png
>
> How different the Hbonds are calculated in VMD from chimera.. I guess
> both should produce approximately same results.

this is just a guess and actually the outcome is not surprising.
there are about as many variants in defining hydrogen bonds as
there are groups researching it. some of the differences are quite
subtle, but can result in significant differences in the absolute
values (and people fight over it). in my personal opinion, this is
a useless endeavor, since the concept of hydrogen bonds is a
phenomenological one in the first place and thus no criterion is
an "absolute" one, but regardless of the individual definition,
they all produce the same trends and that is the important result.
especially when using empirical classical force fields to begin with.

> The Chimera results are convincing as they produce the following

why?? to me the VMD result looks more realistic. you have to ask
the chimera folks how they define a hydrogen bond, and then you
can apply those definitions to VMD, if you think you need it.
as i wrote above, i personally believe that you are putting far
too much weight into some absolute number.

cheers,
    axel.

> output where the separation between D and A was less than 3A. Can we
> get a similar hbonds statistics for a given snapshot of a trajectory
> in VMD(say at start position). Chimera showing me 38 bonds while VMD
> showing a max of 24 bonds in file hbonds.dat at beginning of the
> trajectory .
>
> Thank you for your help.
> S
>
> The chimera results are:
>
> Finding intermodel H-bonds
> Finding intramodel H-bonds
> Constraints relaxed by 0 angstroms and 20 degrees
> Models used:
> #0 I27-smd-cv-0.01Aps.dcd
>
> H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
> LYS 6 N GLU 24 O LYS 6 HN 2.991 2.045
> LYS 6 NZ GLU 22 OE1 LYS 6 HZ2 2.734 1.704
> LEU 8 N SER 80 OG LEU 8 HN 2.972 2.006
> VAL 13 N LYS 85 O VAL 13 HN 2.900 1.917
> GLY 16 N CYS 63 O GLY 16 HN 2.616 1.640
> ALA 19 N LEU 60 O ALA 19 HN 2.698 1.737
> PHE 21 N LEU 58 O PHE 21 HN 2.735 1.706
> ILE 23 N HSD 56 O ILE 23 HN 3.034 2.093
> GLU 24 N LYS 6 O GLU 24 HN 2.975 1.983
> LEU 25 N LYS 54 O LEU 25 HN 2.826 1.818
> LEU 36 N GLN 39 O LEU 36 HN 2.807 1.817
> SER 44 N CYS 47 O SER 44 HN 2.875 1.978
> GLU 48 N ILE 59 O GLU 48 HN 2.791 1.928
> ILE 50 N ILE 57 O ILE 50 HN 3.021 2.078
> LYS 54 NZ GLU 24 OE2 LYS 54 HZ2 2.693 1.613
> LYS 55 NZ GLU 22 OE1 LYS 55 HZ1 2.581 1.708
> LYS 55 NZ GLU 24 OE1 LYS 55 HZ2 2.621 1.675
> HSD 56 N ILE 23 O HSD 56 HN 2.793 1.823
> LEU 58 N PHE 21 O LEU 58 HN 2.649 1.682
> ILE 59 N GLU 48 O ILE 59 HN 2.912 1.897
> LEU 60 N ALA 19 O LEU 60 HN 2.737 1.723
> HSD 61 N ASP 46 O HSD 61 HN 3.026 2.098
> HSD 61 ND1 THR 18 OG1 HSD 61 HD1 2.901 2.025
> CYS 63 N GLU 17 O CYS 63 HN 3.069 2.046
> CYS 63 SG GLU 17 O CYS 63 HG1 3.297 2.057
> MET 67 N GLN 64 O MET 67 HN 3.084 2.107
> THR 68 OG1 LEU 65 O THR 68 HG1 2.885 1.905
> GLY 69 N LEU 84 O GLY 69 HN 3.078 2.184
> VAL 71 N ALA 82 O VAL 71 HN 3.025 2.129
> SER 72 N LYS 35 O SER 72 HN 3.110 2.132
> PHE 73 N SER 80 O PHE 73 HN 2.816 1.900
> GLN 74 N GLN 33 O GLN 74 HN 2.863 1.847
> GLN 74 NE2 SER 72 OG GLN 74 HE21 2.880 1.968
> ALA 75 N ALA 78 O ALA 75 HN 2.888 1.972
> LEU 84 N GLY 69 O LEU 84 HN 2.945 2.061
> LYS 85 N VAL 11 O LYS 85 HN 2.901 1.956
> LYS 87 N VAL 13 O LYS 87 HN 2.854 1.833
> LYS 87 NZ GLU 12 OE2 LYS 87 HZ2 2.769 1.686 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com 
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.