Thank you Dan,
My oversight. I had run previously nativecontacts with 2 masks as shown below.
parm complex_solv.prmtop
parm 4fqt_new.pdb
trajin prod_0-45ns.nc
reference 4fqt_new.pdb parm 4fqt_new.pdb [struct0]
nativecontacts name NC1 :76-80,88-92,96-97,114,202,206,214-218,222,223&!.H= :0VA&!.H= \
byresidue out nc.all.res.dat mindist maxdist \
distance 4.5 reference map mapout resmap.gnu \
contactpdb cont-0VA.pdb \
series seriesout native.dat
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?
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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Received on Thu Feb 11 2016 - 16:00:03 PST
