Hi,
On Thu, Aug 15, 2013 at 1:10 AM, anu chandra <anu80125.gmail.com> wrote:
> Here is the input script I used.
> hbond lig_donor out hb_LIG_donor.dat angle 120 dist 3.5 donormask :294 acceptormask :25,64,65,67,68,69,70,99,102,103,105,106,109,110,140,143,144,147,158,160,165,167,180,182,183,186,266,267,269,270,273,279,284,288
>
> Why hydrogen atoms are considered in the acceptor?. Does the calculation
> looking for the H....H-Donor distance here (manual says distance between
> heavy atoms)?. Why carbon atoms are considered here, evnethough the
> critirion is "“hydrogen bonds are FON” ?
Only automatic searches proceed by the "FON" criterion. As stated in
the manual, when you use 'donormask', valid donors are considered to
be any atoms in the specified mask that are bonded to hydrogen (if you
want you can also use 'donorhmask' to specify what the donor "H" atoms
should be as well). The same is true when you use 'acceptormask';
atoms in the mask you specify are considered valid acceptors. In this
case cpptraj is only doing what you tell it to do. If you want to e.g.
restrict your donors to only F, O, and N atoms bonded to hydrogen in
residue 294 you would specify your 'donormask' as "donormask
:294.F=,O=,N=".
Hope this helps,
-Dan
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Thu Aug 15 2013 - 08:00:02 PDT
