Re: [AMBER] Does minimization require for average pdb structure extract from 2drms plot using CPPTRAJ AMBER 16

From: priya murugan <priyamurugan943.gmail.com>
Date: Tue, 26 Oct 2021 18:15:58 +0800

Thank you very much Dr Adrian for the suggestion. Would definitely consider
your suggestion.
gratefully received.

Thanks & Regards

*PRIYA MURUGAN *

On Mon, Oct 25, 2021 at 10:52 PM Adrian Roitberg <roitberg.ufl.edu> wrote:

> Hi Priya
>
> That script is not for a 2drms, it is just a simple 1D rmsd versus the
> initial frame, and then the does average.
>
> Once you get the average, yes, you need to minimize it. The process of
> averaging can create some weird structures.
>
> I would recommend a different path: Compute the average and THEN
> recalculate the RMSD of the trajectory against the average pdb. Look for
> what frame is closest to the average (lowest rmsd value), extract it,
> and minimize THAT frame.
>
> Adrian
>
>
> On 10/24/21 10:23 PM, priya murugan wrote:
> > [External Email]
> >
> > Hi researcher,
> >
> > I'm really looking for your guidance and help in order for me to pursue
> my
> > next step in computational work. I'm new to computational work and keen
> to
> > learn more. 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 *
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> >
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwICAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=25jBCvJrkndhFtaLxZ0Uokk3VCTvdbWtce26Et97R6I&s=EnQfsYTOdENF2HPhvz_4Qbf38Tu9JjE86wFvqUcwVEo&e=
>
> --
> Dr. Adrian E. Roitberg
> V.T. and Louise Jackson Professor in Chemistry
> Department of Chemistry
> University of Florida
> roitberg.ufl.edu
> 352-392-6972
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Oct 26 2021 - 03:30:02 PDT
Custom Search