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 Mon Sep 25 2023 - 02:30:01 PDT
