P.S.S I've already tried to use distance based selection: to select
all residues within 8A of ligand + ligand itself for the calculations,
hbond contacts (:lig<:8)|:lig
but this mask did not work with hbond ;-)
Il giorno mer 14 dic 2022 alle ore 16:19 Enrico Martinez
<jmsstarlight.gmail.com> ha scritto:
>
> P.S. after examining pdb of the complex produced by tleap I found that
> the chain information was absent and the both protomers are separated
> just by TER record (this is why nointramol did not work ... )
> the only dirty solution that could work for 2 different protein is to
> use the number of the residues for the smaller protein e.g. 1-300|:lig
> would work equally fine for protein with 300 and 304 amino acids
> (assuming that the ligand never establishes contacts with residues
> 301-304 in the case of bigger protein..
> May we have a more elegant solution ? ;-)
>
> Il giorno mer 14 dic 2022 alle ore 15:58 Enrico Martinez
> <jmsstarlight.gmail.com> ha scritto:
> >
> > 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 - 08:30:02 PST
