.. so what I have already tried:
# using the first snapshot (Begining of simulation) to calculate evolution
of the distance for the ligand- DOES NOT WORK
distance lig-dist :lig :lig ref first.pdb out Distance.LIG.xvg
# calculate hydrogen bonds between :lig and all residues located within 10
A of the lig. CALCULATE always 0 H-bonds
hbond contacts :lig<:10.0|:lig out HBonds.xvg nointramol time 0.05
I would appreciate any help !!
Enrico
Il giorno lun 15 lug 2024 alle ore 16:31 Enrico Martinez <
jmsstarlight.gmail.com> ha scritto:
>
> Dear Amber Users !
>
> Dealing with the analysis of protein-ligand system I am using the
> following script to
>
> # 1 - calculate distance of the ligand from the residue involved in the
> interaction
> distance lig-glu166 :lig :166.N out distanceLIG.xvg
> # 2 - calculate number of hydrogen bonds between ligand and protein
> hbond contacts :1-300|:lig out hydrogenbonds.xvg nointramol
>
> My question is it possible
> 1 - calculate distance taking into account initial position of the ligand
> and the position during the simulation (without definition of the active
> site residue ) ?
>
> 2 - calculate the number of hydrogen bonds between ligand and all residues
> around 10 A from the ligand (so providing only a geometrically-based amber
> mask without explicit definition of any selection related to number of
> amino acids of protein) ?
>
> Many thanks in advance !
>
> Enrico
>
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Received on Tue Jul 16 2024 - 01:30:02 PDT
