Thank you, Bill. I agree.
I haven't given the topology or connection files, but why the average structure looks more right. Does "rms first" do something?
________________________________
From: Bill Ross <ross.cgl.ucsf.edu>
Sent: Monday, May 13, 2019 9:50 PM
To: amber.ambermd.org
Subject: Re: [AMBER] Average structure vs Individual frames
Have you given pymol any topology info, e.g. in a prmtop, or pdb with
CONECT records? If not, poor pymol is just doing the best it can based
on distance, I suspect.
Bill
On 5/13/19 6:16 PM, Yin, Guowei wrote:
> Hello all,
>
> My protein contains GDP and Mg2+. After the simulation, I look up the individual frames and the average structure over the 50 ns. I found in the individual frames the Mg2+ stays close to the phosophates of GDP and leads to the artificial bonds recognized by the PyMol. But in the average structure, the distance looks fine and no artificial bonds by PyMol. I attached the screenshot below. This is something with the processing?
>
> The parameters used for Mg is:
> Oelschlaeger et al JMB 2007 Mg dummy and MD6.
>
> When I generate the final trajectory, I used the unwrap as:
>
> unwrap :1-169
>
> center :1-169 mass origin
>
> image origin center familiar
>
> and the way I generate the average structure is:
>
> cpptraj ../proteinA.top <<eof
>
> trajin ./proteinA.mdcrd 25000 50000 1
>
> rms first
>
> average proteinA.avg.pdb pdb
>
>
> =====
>
> The average structure
> [image.png]
>
> individual frames:
>
> [cid:a43a94a8-7a83-41c2-ba22-e46fdddcbf82]
>
>
>
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Received on Mon May 13 2019 - 19:30:03 PDT
