Thank you very much Dr Anselm Horn. Useful suggestion and gratefully
received.
On Mon, 25 Oct 2021, 17:33 Dr. Anselm Horn, <anselm.horn.fau.de> wrote:
> Priya,
>
> please note that an averaged pdb file may contain an unnatural structure
> due to averaging e.g. two conformational side chain minima into an
> high-energetic transistion state-like structure. Thus, it is not well
> suited as a structure representative of your MD simulation.
>
> An alternative would be to use clustering of that (part of the)
> trajectory you are interested in, and then use the most populated
> cluster representative structure for your further workflow.
> Clustering is also implemented in cpptraj, and therefore ready for your
> use (see the comprehensive Amber manual).
>
> Whether a minimization is needed before docking, others may know better.
> Personally, I'd do a short relaxation (= minimization) of the structure.
> The best way IMHO, however, would be to look for published papers that
> did MD with subsequent docking to see what exact workflow they used.
>
> Regards,
>
> Anselm
>
> Bioinformatik | NHR.FAU
> Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
> Germany
>
>
> Am 25.10.2021 um 05:27 schrieb priya murugan:
> > Hi researcher,
> >
> > I'm really looking for your guidance and help in order for me to pursue
> my
> > next step in computational work. Currently, I'm using AMBER 16 to do
> > Molecular Dynamic (MD) simulation and trajectory analysis. The protein
> I'm
> > working with is 5IBE. I used CPPTRAJ to extract RMSD'd PDB's from
> > trajectories. I extract specific frames of the trajectory in a 2drms
> plot,
> > to generate the average structure in PDB format. This is the script I
> used
> > to generate the average PDB structure from a 2drms plot.
> >
> > cpptraj.in file
> > trajin 5IBE_heme_md_pc.binpos 2100 2500
> > rms first mass .C,CA,N
> > average 5IBE_heme_md_pc_2100-2500.pdb pdb
> >
> > 2100-2500 is the frame value from the 2drms plot.
> >
> > My question is do I need to minimize the average PDB structure that I got
> > from CPPTRAJ analysis before continuing with molecular docking? Is that
> ok
> > If I continue using this average PDB structure for the docking process
> > without minimization? Please let me know, I need some clarification.
> >
> > I would be grateful for every suggestion that will be given to me.
> >
> >
> > Thanks & Regards
> > *PRIYA MURUGAN *
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
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Received on Mon Oct 25 2021 - 03:30:02 PDT
