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
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Received on Tue Jun 26 2012 - 08:30:03 PDT
