It looks fine to me, but there's no substitute for visualizing it yourself
to make sure.
All the best,
Jason
On Tue, Jun 26, 2012 at 11:00 AM, Olena Dobrovolska <
olena.dobrovolska.biotech.ntnu.no> wrote:
> Thanks Jason, since I am not a specialist here, would you please have a
> look and correct?
> I have made a folder where I copied all 20 minimized structures, prmtop
> file of the first one, and made the file called avemin.ptraj, in which I
> put this:
>
> trajin min1.pdb
> trajin min2.pdb
> trajin min3.pdb
> trajin min4.pdb
> trajin min5.pdb
> trajin min6.pdb
> trajin min7.pdb
> trajin min8.pdb
> trajin min9.pdb
> trajin min10.pdb
> trajin min11.pdb
> trajin min12.pdb
> trajin min13.pdb
> trajin min14.pdb
> trajin min15.pdb
> trajin min16.pdb
> trajin min17.pdb
> trajin min18.pdb
> trajin min19.pdb
> trajin min20.pdb
>
> rms first out rms .CA, C, N
> average 1.pdb pdb
>
> Is it correct?
> ________________________________________
> From: Jason Swails [jason.swails.gmail.com]
> Sent: 26 June 2012 15:55
> To: AMBER Mailing List
> Subject: Re: [AMBER] calculation of the average structure
>
> You can use ptraj or cpptraj to do it. Load all of the structures in via
> the "trajin" command, align them with an RMSD command, and then calculate
> the average structure (which you can dump as a PDB or some similar file
> format).
>
> HTH,
> Jason
>
> On Tue, Jun 26, 2012 at 8:15 AM, Olena Dobrovolska <
> olena.dobrovolska.biotech.ntnu.no> wrote:
>
> > Hi everybody,
> >
> >
> >
> > Do you know how to calculate the average protein structure from the 20
> > minimized conformers in AMBER?
> >
> > (I tried to make it in MOLMOL, but the obtained avemin structure contains
> > extra atoms.)
> >
> >
> >
> > Thanks,
> >
> > Olena
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> 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
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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AMBER mailing list
AMBER.ambermd.org
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Received on Tue Jun 26 2012 - 08:30:04 PDT
