Dear Amber Users!
I am using the following command to calculate hydrogen bonds between
protein and ligand during molecular dynamics:
hbond contacts :1-304|:lig out hb.xvg avgout HBavg.log nointramol time 0.05
It works well in the case of the dimer containing 2 monomers of 304
amino acids + ligand bound to the first monomer.
But when I apply it (using the same script) for a slightly different
system (still containing ligand bound to the first monomer) it
produces wrong results in the case when the monomer consists of less
than 304 amino acids. In this case the intramolecular hydrogen bonds
(probably between two monomers) are also taken into account (in spite
of the "nointramol" option provided for hbond):
Here is the output of the command for the complex with the monomer of
301 residues:
#Acceptor DonorH Donor Frames Frac
AvgDist AvgAng
GLU_286.OE2 ARG_304.HH22 ARG_304.NH2 48 0.9600
2.7908 163.3124
GLU_286.OE1 ARG_304.HH12 ARG_304.NH1 47 0.9400
2.7610 163.1736
GLY_126.O ARG_304.HH21 ARG_304.NH2 40 0.8000
2.8054 162.3148
GLY_302.O SER_138.HG SER_138.OG 33 0.6600
2.7080 161.3211
lig_602.N2 HIE_162.HE2 HIE_162.NE2 17 0.3400
2.8804 145.3652
GLU_165.OE1 ALA_301.H2 ALA_301.N 16 0.3200
2.6688 152.8132
GLU_165.OE1 ALA_301.H3 ALA_301.N 15 0.3000
2.7332 158.9117
GLU_165.OE1 ALA_301.H1 ALA_301.N 11 0.2200
2.7174 159.1036
lig_602.O GLY_142.H GLY_142.N 10 0.2000
2.8756 163.4150
ARG_136.O ARG_304.HH11 ARG_304.NH1 8 0.1600
2.8000 150.3220
GLU_286.OE1 ARG_304.HH22 ARG_304.NH2 4 0.0800
2.9431 146.3416
PHE_139.O ALA_301.H2 ALA_301.N 2 0.0400
2.6759 144.8209
PHE_139.O ALA_301.H3 ALA_301.N 1 0.0200
2.6814 136.4836
PHE_139.O ALA_301.H1 ALA_301.N 1 0.0200
2.9507 137.1555
GLU_165.OE2 ALA_301.H3 ALA_301.N 1 0.0200
2.9557 158.3515
lig_602.N3 HIE_162.HE2 HIE_162.NE2 1 0.0200
2.9906 172.5356
Could you provide a more flexible atom mask for the selection e.g. to
select all amino acids in the chain A or alternatively ignore any
protien-protein interactions (e.g. between 2 monomers)?
Many thanks in advance
Cheers
Enrico
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Received on Wed Dec 14 2022 - 07:00:03 PST
