AMBER Archive (2004)

Subject: Re: AMBER: average structure using ptraj

From: NI AI (aini_at_UMDNJ.EDU)
Date: Fri Jul 02 2004 - 10:15:53 CDT

Dear Dr. Cheatham,

  Thank you very much for your answer! I striped water and counter ions and
used modified script. The minimization went through. However, this
minimization is done in vaccum since I don't know how to put water and ions
back to the system. Do I need to read in average.pdb to xleap and prepare
another .top and .crd file for minimization? or you have different way to do
that?
Thank you very much!
aini

On Thursday 01 July 2004 13:40, Thomas E. Cheatham, III wrote:
> > I tried to use ptraj in AMBER7 to average the last 200 frame of my MD
> > run. The script I used:
> >
> > traj AR.top << EOF
> > trajin AR.md7.crd 300 500
> > center :1-250
> > image center familiar
> > average average.rst restrt
> > EOF
> >
> > Then I did one more miminization for 5000 steps. It didn't go through.
> > The EEL term became ********.
>
> It is always a good idea to "look" at the structure. Note that rotating
> groups (such as methyls) spin rapidly and this can lead to overlapping
> atoms upon coordinate averaging.
>
> Also note that the average command does not do any fitting of the
> structure prior to averaging, so if the whole molecule is rotating, this
> may lead to overlapping atoms.
>
> Finally, averaging water positions or mobile ions will also lead to
> overlapping; if you have ions or water in the system, as they move across
> the box rapidly, this will lead to a big blob of water/ions in the center
> overlapping the solute (and hence high VDW and EEL energies).
>
> So, I would modify your script as follows:
>
> traj AR.top << EOF
> trajin AR.md7.crd 300 500
> center :1-250
> image center familiar
> rms first mass out rms.dat :1-250
> average average.rst restrt
> average average.pdb pdb
> EOF
>
> ...and take a look at the average.pdb.
>
> Likely, if you want the average structure for minimization, you will have
> to strip the water/ions and then (optionally) add them back in.
>
> Good luck.
>
>
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