I gotcha, thank you very much !
maybe there is another way to specify any residue around lig or just all
protein residues w/o definition of the amino acid numbering ?
Many thanks in advance !!
Enrico
Il giorno mar 16 lug 2024 alle ore 18:03 Martin Juhás <juhasm.faf.cuni.cz>
ha scritto:
> Hi,
>
> As far as I know, there is no "dynamic" distance-based selection. You can
> define selection by distance, but it does not change during the analysis
> once defined.
> Did you try nativecontacts analysis? This is used to follow contacts based
> on what is observed at the beginning.
>
> If you want dynamic-based selection for analysis, I think VMD software
> from
> https://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD
> allows it.
>
> Please, anyone, correct me if I am wrong...
>
> Hope this helps.
>
> Martin
>
> -----Original Message-----
> From: Enrico Martinez via AMBER <amber.ambermd.org>
> Sent: Tuesday, July 16, 2024 10:05 AM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] Analysis of protein-ligand interactions
>
> [EXTERNAL EMAIL]
>
>
> .. 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 Wed Jul 17 2024 - 03:00:02 PDT
