Dear Amber users,
just to precise my question, I've just used a simplified script with
the aim to calculate contact map for protein-protein interaction
nativecontacts name contacts :1-100 :101-201 map mapout resmap.gnu
Eventually this produced a gnu file but when I tried to visualize it
with gnuplot it produced nothing.
could you suggest a proper visualisation technique for such output format ?
Many thanks in advance
Enrico
Il giorno lun 25 set 2023 alle ore 11:20 Enrico Martinez
<jmsstarlight.gmail.com> ha scritto:
>
> Dear Amber users,
>
> I would like to calculate and visualize a contact map by means of
> cpptraj with the aim to determine residues being in contacts during
> molecular dynamics.
>
> I've found only the following example, which might work for a protein
> - ligand case
>
> nativecontacts name NC1 :0VA&!.H= \
> byresidue out nc.all.res.dat mindist maxdist \
> distance 3.0 reference map mapout resmap.gnu \
> contactpdb cont-0VA.pdb \
> series series out native.dat
>
> should something be modified besides the selection areas e.g. for the
> case when I need to calculate contacts for dimeric water-soluble
> protein ?
>
> Many thanks in advance
>
> Yours sincerely
>
> Enrico
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Received on Tue Sep 26 2023 - 07:00:02 PDT
