VMD-L Mailing List

From: lanhua (lh2122_at_columbia.edu)
Date: Fri May 04 2007 - 20:57:35 CDT

Hi,
    I am a little bit confused about "Known Issue: The output of hbonds cannot be considered 100% accurate if the donor and acceptor selection share a common set of atoms" for "measure hbonds" in the VMD manual. I have two cases:
    1. >set sel [atomselect top "water"]
>measure hbonds 1.4 60 sel
       So for this case the donor and acceptor share a common set of atoms, the output can't be 100% accurate.

    2. >set sel1 [atomselect top "resname URE and name O"]
>set sel2 [atomselect top "resname URE and name N1 N2"]
       How about this case? I am confused that these two selections share common solvent molecules (urea). Can the output be 100% correct?

Bests,
Lan