VMD-L Mailing List

From: Mgr. Lubos Vrbka (lubos.vrbka_at_uochb.cas.cz)
Date: Wed Jan 18 2006 - 10:13:29 CST

hi guys,

i encountered an issue with measure hbonds command:

i use
set ow [ atomselect top "name OW" ]

measure hbonds 2.9 30.0 [ atomselect top "index 5" ] $ow
5 is one of the oxygens contained also in the 'ow' list
this gives me correct answer (i checked it in the structure)

{5 5} {191 473} {1 0}

however when i reverse the order
measure hbonds 2.9 30.0 $ow [ atomselect top "index 5" ]
i get "more than i expected":

{989 5 5 815} {5 191 473 5} {989 1 0 810}

according to the manual it should report index 5 as an acceptor only...
since there are no other atoms in the 'acceptor' list that could mix
together with atoms from 'donor' list.
is this the case where overlapping donor and acceptor cause problems (as
reported in the manual)? in my case i want to get all hydrogen bonds
that a given molecule forms, i thought i could concatenate outputs from
both abovementioned commands, but it doesn't seem to work... or is the
second command exactly the thing i'm looking for? will it behave the
same every time?

thanks for help. regards,
lubos 

-- 
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Mgr. Lubos Vrbka
Center for Biomolecules and Complex Molecular Systems
Institute of Organic Chemistry and Biochemistry
Academy of Sciences of the Czech Republic
Prague, Czech Republic
http://www.molecular.cz/~vrbka
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