Re: use of 'measure hbonds'

Date: Thu Jun 12 2008 - 11:08:12 CDT

Is this u actually wrote the command? If it is so, its wrong. You
selected selections as sel and sel1, and u asked to measure hbond between
$sel1 and $sel2.
It might be taking some pre-selected selection.

  On Thu, 12 Jun 2008, DEEPESH AGARWAL wrote:

> Dear NAMD users,
> I want to know whether some residues in my protein are forming h-bonds
> with water. What should be the appropriate cut-off and angle, and what
> factors do these two depend upon??
> Also i read in NAMD user's guide abt the usage according to which
> first atomselection should be for donors and second for acceptors, and
> by default only non-hydrogen atoms are considered so I did----
>> set sel1 [atomselect top "protein and resid X"]
>> set sel [atomselect top "water"]
>> measure hbonds 5 150 $sel2 $sel1
> Is this correct?
> Three lists r generated. The first index in my first list is of
> hydrogen which i suppose should not be and in the last list i m
> getting indices of atoms other than hydrogens too. Could anyone tell
> me the correct interpretation of these lists. Thanks in advance.
> Deepesh

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