On Thu, Feb 11, 2016 at 4:38 PM, George Tzotzos <gtzotzos.me.com> wrote:
> I’m now inspecting the gnu plot and I do get some native contacts with the cutoff shown in the script. My last question has to do with the heat map. Range shown is 0-6. I assume it is Angstrom. Am I correct?
The manual is unfortunately not clear on this. Each cell in the maps
are the total number of contacts between the two atoms/residues (in
your case residues since 'byresidue' is specified) normalized by the
total number of frames. So a value of 6 means that on average there
are 6 contacts between the two residues.
Thanks for pointing that out.
-Dan
>
> Thanks again for your help
>
> George
>
>> On 12 Feb 2016, at 00:10, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>
>> On Thu, Feb 11, 2016 at 2:49 PM, George Tzotzos <gtzotzos.me.com <mailto: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/ <http://home.chpc.utah.edu/~cheatham/>
>> (801) 587-9652
>> (801) 585-6208 (Fax)
>>
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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 - 16:00:04 PST
