VMD-L Mailing List

From: snoze pa (snoze.pa_at_gmail.com)
Date: Thu Jan 28 2010 - 17:32:10 CST

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.

The Chimera results are convincing as they produce the following
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