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 - 07:30:02 PST
