On Thu, Feb 11, 2016 at 2:49 PM, George Tzotzos <gtzotzos.me.com> wrote:
> I have two questions: (a) how are native contacts defined in cpptraj (couldn’t find this info in the manual - my oversight?)
I think the explanation in the Amber 15 manual is pretty clear
(section 29.9.36 'nativecontacts', page 582):
'Define and track “native” contacts as determined by a simple distance
cut-off, i.e. any atoms which are closer than <cut> in the specified
reference frame (the first frame if no reference specified) are
considered a native contact. If one mask is provided, contacts are
looked for within <mask1>; if two masks are provided, only contacts
between atoms in <mask1> and atoms in <mask2> are looked for (useful
for determining intermolecular contacts).'
> and (b) is there something wrong with the input script above.
You stated that you wanted to identify ligand contacts (presumably
with the receptor), but you only provided a single mask that defines
the ligand (0VA) only; the way 'nativecontacts' works this will only
report contacts within that mask. If you want to look for contacts
between the ligand and receptor you should provide a second mask that
defines the receptor as well.
Hope this helps,
-Dan
>
> Thanks in advance for any suggestions
>
> Regards
>
> George
>
>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Feb 11 2016 - 15:30:03 PST
