I used the nativecontacts command of cpptraj to identify ligand contacts within the receptors binding cavity in the course of a 100 ns MD trajectory. The ligand name is 0VA.
I followed the instructions of the Amber 2015 manual to generate the following input script:
parm complex_solv.prmtop
parm 4fqt_new.pdb
trajin prod_0-100ns.nc
reference 4fqt_new.pdb parm 4fqt_new.pdb [struct0]
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
No native contacts were identified and only 3-4 non-native contacts are shown in the gnu plot.
This is rather strange as pairwise per-residue decomposition in MMPBSA shows several interactions (mainly vdW but also a few electrostatic) with the ligand and binding site residues.
I have two questions: (a) how are native contacts defined in cpptraj (couldn’t find this info in the manual - my oversight?) and (b) is there something wrong with the input script above.
Thanks in advance for any suggestions
Regards
George
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Feb 11 2016 - 14:00:05 PST
