On 10/25/21 2:53 PM, James Kress wrote:
> [External Email]
>
> Why do you minimize the average structure? Won't that minimization just
> result in another, non-average structure?
Yes, but the average structure is bound to be non-physical. For example,
imagine the average structure of a methyl group in a protein. The "free"
rotation of the H atoms means that when averaged, all H will be on top
of each other.
Adrian
>
> Jim
>
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> -----Original Message-----
> From: Adrian Roitberg <roitberg.ufl.edu>
> Sent: Monday, October 25, 2021 10:52 AM
> To: amber.ambermd.org
> Subject: Re: [AMBER] Does minimization require for average pdb structure
> extract from 2drms plot using CPPTRAJ AMBER 16
>
> 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 *
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> --
> Dr. Adrian E. Roitberg
> V.T. and Louise Jackson Professor in Chemistry Department of Chemistry
> University of Florida roitberg.ufl.edu
> 352-392-6972
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Dr. Adrian E. Roitberg
V.T. and Louise Jackson Professor in Chemistry
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Mon Oct 25 2021 - 12:30:02 PDT
