Hi,
The nativecontacts command you're looking for will be something like this:
nativecontacts <protein mask> <graphene mask> mindist out contacts.dat
In contacts.dat there will be a column of data named X[mindist], which is
the closest distance between any atoms in the two masks. In the example
below this is column #4:
#Frame NC1[native] NC1[nonnative] NC1[mindist] NC1[maxdist]
1 31 0 3.6912 16.2018
2 31 1 3.7418 16.3238
3 28 1 3.7696 15.5250
4 28 1 3.8041 15.5250
5 29 1 3.7595 15.1851
Hope this helps,
Christina
On Tue, Oct 20, 2015 at 12:20 PM, Krantzman, Kristin D <KrantzmanK.cofc.edu>
wrote:
> Dear Hai and Amber users,
> I do know how to calculate the distance between the center of mass of the
> graphene surface and the center of the mass of the protein. However, I
> wanted to calculate the distance with the CLOSEST heavy atom in the
> protein. The Amber15 manual referred to the nativecontact command under
> the mindist command. I would like guidance in how to use this command to
> calculate the minimum distance.
> Thanks again, Kristin
> ________________________________________
> From: Hai Nguyen [nhai.qn.gmail.com]
> Sent: Tuesday, October 20, 2015 2:09 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Measuring distance between protein and graphene
> surface
>
> I guess you can use cpptraj:
>
>
> https://urldefense.proofpoint.com/v2/url?u=http-3A__ambermd.org_tutorials_analysis_tutorial0_&d=CwICAg&c=7MSSWy9Bs2yocjNQzurxOQ&r=rDr-VDoXCKpr5ouXXYSZkHF6q5gU19w8m7W8WZccZ7U&m=Xkk5aGQL3IFUzM7WUXU-zK9eI7OCst60LOv0Kg0svG0&s=dOS9F7lEGj-IJ9S7H9COw_6ez-nmuplZpHwTJynbs7U&e=
>
> You can check amber 15 manual for further info.
>
> Hai
>
>
> On Tue, Oct 20, 2015 at 2:01 PM, Krantzman, Kristin D <KrantzmanK.cofc.edu
> >
> wrote:
>
> > Greetings,
> > I have performed a md simulation of a protein adsorbed to a graphene
> > surface with pmemd. I would like to calculate the distance between the
> > protein and the graphene surface. Could you please guide me on how to
> > proceed? Thank you in advance.
> > Best, Kristin D. Krantzman
> > _______________________________________________
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> > AMBER.ambermd.org
> >
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=CwICAg&c=7MSSWy9Bs2yocjNQzurxOQ&r=rDr-VDoXCKpr5ouXXYSZkHF6q5gU19w8m7W8WZccZ7U&m=Xkk5aGQL3IFUzM7WUXU-zK9eI7OCst60LOv0Kg0svG0&s=eFqTkketNSNhGnWdLdrQXTsIBT2r7yU3ksfVvVNNTQg&e=
> >
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>
--
---------------------------------------------------------------------------------------
Christina Bergonzo, PhD
Postdoctoral Researcher
Department of Medicinal Chemistry, University of Utah
30 South 2000 East, Rm. 201
Salt Lake City, UT 84112-5820
Office: L.S. Skaggs Pharmacy Research Institute, Rm.4290
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652 / Fax: (801) 585-6208
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Received on Tue Oct 20 2015 - 12:30:04 PDT
