Hi AMBER community,
I have a protein/ligand system and want to calculate the probability of
heavy-atom to heavy-atom contacts between protein residues within 4
angstroms of the ligand throughout the trajectory. For this, I used the
"nativecontacts" command of AmberTools with the selection :LIG&!.H=
:1-564&!.H= and a VMD Tcl script with protein and noh and same residue as
within 4 of (resname LIG and noh).
Cpptraj command:
cpptraj
nativecontacts name NC1 :LIG&!.H= :1-564&!.H= \
writecontacts residueContactInfo.dat resout contact_residue_pairs.dat \
byresidue out Num_native_nonNative.dat mindist maxdist \
distance 4.0 reference map mapout resmap.gnu \
contactpdb nativeContact.pdb series seriesout native.dat
Surprisingly, I am getting different results from these calculations. I am
a bit confused about which one gives me the actual results.
Any help would be appreciated.
Thank you
Fulbabu
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Apr 29 2024 - 09:30:02 PDT
