Hi Sinjini,
I dont think there is anything wrong with just picking the mask of the
residues you consider relevant and fitting to that. Have you tried, i.e.
does that give you problematic results? If you want, you could first
compute RMSF values for the whole protein and then define a mask of
rms-fitting residues based on the amount of fluctuation they undergo,
excluding the mobile loop residues.
Kind Regards,
Thomas
On Wed, Jul 26, 2023 at 3:37 PM Bhattacharjee, Sinjini via AMBER <
amber.ambermd.org> wrote:
> Hi AMBER community,
>
> I am working with a membrane-protein system which has numerous loops. I
> want to obtain the best aligned MD snapshots but only fit the helices and
> beta sheets and exclude the loop regions.
>
> I have the following questions:
>
> What is the best way to do this in cpptraj?
> Should I use the ‘align’ keyword along with the atom mask for everything
> excluding loops ?
>
> Also, what is the difference between the ‘align’ and ‘rms’ fit option for
> the above purpose?
>
>
> Many thanks for your suggestions!
>
> Best,
>
> —
> Sinjini Bhattacharjee
>
> PhD Student
> Molecular Theory and Spectroscopy
> Max-Planck-Institut für Kohlenforschung
> 45470 Mülheim an der Ruhr, Germany
>
> email: bhattacharjee.kofo.mpg.de<mailto:bhattacharjee.kofo.mpg.de>
> ---
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
*Dr. Thomas Steinbrecher*
Principal Scientist CADD
Roche Pharma Research and Early Development
Roche Innovation Center Basel
F. Hoffmann-La Roche Ltd
Bldg. 092/3.92
Grenzacherstrasse 124
4070 Basel
Switzerland
Phone +41 61 682 1319
mailto: thomas.steinbrecher.roche.com
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Received on Wed Jul 26 2023 - 07:30:02 PDT
