VMD-L Mailing List

From: Andrew Dalke (dalke_at_ks.uiuc.edu)
Date: Wed Mar 05 1997 - 09:37:55 CST

> I have only one problem, I can't see H-bonds.

  Only one? I've got more than that ... :)

  There are several reasons why you might not see H-bonds, but the
most likely is that didn't find any. The default angle and distance
criterion in VMD are too small, so try increasing the angle value from
20 to 30 degrees and the distance value from 3 to 4. Looking at
9pti with HBonds shows nothing with the default and several with those
parameters increased.
  You should also increase the with of the hydrogen bonds from 1 to 2.
(On most SGIs you can't make it any wider than that, as described in
the manual.) We should also add a way to use cylinders in addition to
(instead of?) lines so they can be made more obvious.

  Speaking of hydrogen bonds, does anyone here know of a freely
redistributable package that computes h-bonds well and rapidly?
I know about HBPlus, but it isn't redistributable. Both DSSP and
STRIDE compute mainchain h-bonds of proteins, but I would like
something which can report h-bonds in nucleic acids as well.

                                                Andrew Dalke
                                                dalke_at_ks.uiuc.edu