Hi Shivani,
that is hard to answer just based on the number, but if you expect to see a
large conformational change in a protein, something like a channel opening
or closing for example, that would be more than 3A RMSD and more
importantly likely way beyond the kind of change MD simulations can
accomplish. Without knowledge of what change you expect, it will generally
be very hard to simulate a physiologically relevant major conformational
change by brute force MD.
Kind Regards,
Thomas
On Wed, Feb 28, 2024 at 6:22 PM Godbole, Shivani <ssg5401.psu.edu> wrote:
> I am trying to induce conformational changes with lower pH for which I
> need a higher RMSD value to justify that my system is active at a lower pH
> than the physiological pH. Does 3A justify that conformational change?
>
> I am new at MD simulations and am still learning.
>
> Thank you,
>
> Shivani
>
> *From:* Steinbrecher, Thomas <thomas.steinbrecher.roche.com>
> *Sent:* Wednesday, February 28, 2024 12:17 PM
> *To:* Godbole, Shivani <ssg5401.psu.edu>; AMBER Mailing List <
> amber.ambermd.org>
> *Subject:* Re: [Sender Not Verified] [AMBER] RMSD values are low
>
>
>
> You don't often get email from thomas.steinbrecher.roche.com. Learn why
> this is important <https://aka.ms/LearnAboutSenderIdentification>
>
> Hi Shivani,
>
>
>
> why do you consider this a problem? In general, a stable MD simulation of
> a typical protein will result in RMSD values rising to around 2A over
> several 100ns. Are there conformational changes you expect and do not see
> in your runs? Otherwise, your result may just be in the expected range of
> outcomes.
>
>
>
> Kind Regards,
>
>
>
> Thomas
>
>
>
>
>
> On Wed, Feb 28, 2024 at 6:06 PM Godbole, Shivani via AMBER <
> amber.ambermd.org> wrote:
>
> **Warning** The sender address ("Godbole, Shivani via AMBER" ) can not be
> verified, sender email address could be spoofed. Please take care to
> proceed.
> Hello,
> This is Shivani Godbole. I am running Constant pH Md simulations for my
> proteins. I have noticed the RMSD values after running the cpptraj command
> are quite low (around 3 A). What can be done about this?
> Thank you,
>
> Shivani Sujay Godbole, B. Pharm
> Biomedical Sciences, Ph.D. Student
> Penn State College of Medicine
>
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>
>
>
>
> --
>
> *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
>
--
*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 Feb 28 2024 - 10:00:02 PST
