Hi,
In the GitHub version of cpptraj (
https://github.com/Amber-MD/cpptraj)
a new keyword has been added to 'nativecontacts':
nncontactpdb <file>
which will print out a PDB of the reference frame used to determine
native contacts with the B-factor column assigned a value related to
relative contact strength, with 100 assigned to the strongest contact.
Maybe this is close to what you want?
-Dan
On Wed, Feb 15, 2017 at 9:28 AM, antonio.coluccia.uniroma1.it
<antonio.coluccia.uniroma1.it> wrote:
> Dear all,
> I am in trouble with contact map
> i have done some simulations of my protein embedded into water and a
> organic cosolvents (20%) octaedron boxes.
> At this point i would like to generate a 3D map of frequency
> interaction/contact between the protein and the organic solvent molecules.
> Is it possible by cpptraj? I read something about nativecontact but my
> concerns are about the output, is it possible to have 3d maps by
> nativecontatcs.
>
> Thank you very much,
> any help will be really appreciate.
>
> Antonio
>
> --
> Antonio Coluccia, Ph.D.
> Department of Chemistry and Drugs Tecnology
> La Sapienza University
> Rome 00185
> Piazzale Aldo Moro 5
> antonio.coluccia.uniroma1.it
> mobile: 00393406113351
>
>
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Wed Feb 15 2017 - 08:00:02 PST
