Hi,
What version of cpptraj are you using?
-Dan
On Mon, Sep 17, 2018 at 4:54 PM Sourav Purohit <sour000.gmail.com> wrote:
>
> Hello all,
>
> I am simulating a protein-DNA complex.
> I used the folllowing command to calculate the residue-wise contact map of
> the contacts between the protein and the DNA :
>
> trajin 1-combined.trj
> nativecontacts :1-60 :61-93 byresidue map mapout 1-contact-map.dat
>
> residue id 1-60 correspond to DNA, while 61-93 correspond to protein.
>
> Is the command line correct or is something needed to be added to this.
>
> The output contact map is a 93 X 93 matrix.
> As two masks are specified should we not get a 60 X 33 matrix as the output?
> Does this command also calculate the intra-mask contacts?
>
> Thanks in advance for your help and suggestions.
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Received on Thu Sep 20 2018 - 06:30:03 PDT
