Yes, it has been fitted beforehand since I computed rmsd with the
script shown in the first message.
I also double checked it via calculation with gromacs and it's exactly
the same curve.. :-)
With best regards
Enrico
Il giorno ven 7 lug 2023 alle ore 11:34 Steinbrecher, Thomas
<thomas.steinbrecher.roche.com> ha scritto:
>
> Hi Enrico,
>
> did you do rms fitting beforehand? The atomicfluct command says " Note that RMS fitting is not done implicitly" so you may see an rmsf that includes diffusion of your protein? Otherwise, 9A is a lot but does it match what happens in the trajectory when you visualize it?
>
> Kind Regards,
>
> Thomas
>
> On Fri, Jul 7, 2023 at 10:42 AM Enrico Martinez <jmsstarlight.gmail.com> wrote:
>>
>> Hello Thomas !
>>
>> Thank you very much for your kind reply.
>>
>> Ops sorry actually the command for RMSF was
>>
>> atomicfluct byres out rmsf.xvg @CA
>>
>> Indeed it was about 0.9 nm = 9 A in the most flexible segment ( I
>> enclose the graph...)
>>
>> P.S. Does it take into account the averaged structure from the
>> trajectory or alternatively the first frame for rmsf computing ?
>>
>> Many thanks in advance
>>
>> Enrico
>>
>> Il giorno ven 7 lug 2023 alle ore 09:26 Steinbrecher, Thomas
>> <thomas.steinbrecher.roche.com> ha scritto:
>> >
>> > Hi Enrico,
>> >
>> > do you really mean 0.9A? That is not flexible at all, it should barely be visible as motion when viewing the trajectory.
>> >
>> > Also, from naming your files, you do compute an RMSD over the trajectory, not RMSF values for your atoms, no?
>> >
>> > What is the "time 0.05" for, I could not find that in the manual?
>> >
>> > Kind Regards,
>> >
>> > Thomas
>> >
>> > On Thu, Jul 6, 2023 at 5:44 PM Enrico Martinez via AMBER <amber.ambermd.org> wrote:
>> >>
>> >> Dear Amber users !
>> >>
>> >> Dealing with short md simulation of a very flexible water soluble
>> >> protein, I removes pbc using the following protocol:
>> >>
>> >> # center on the alpha helix located in the middle of protein
>> >> center :125-145 mass origin"
>> >> "image origin center"
>> >> "autoimage"
>> >>
>> >> and then calculate rmsf using
>> >>
>> >> "rms protToFirst @CA,C,O,N,H&!(:WAT|:lig) first out rmsf.xvg mass time 0.05"
>> >>
>> >> From this graph I see that the protein in some parts tends to be very
>> >> flexible (up to 0.9 A) even during 10 ns of the modeling. May the
>> >> protocol responsible for the first part (pbc) affect the calculation
>> >> of the rmsf profile ?
>> >>
>> >> Many thanks in advance
>> >>
>> >> Cheers
>> >>
>> >> Enrico
>> >>
>> >> _______________________________________________
>> >> 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
>
>
>
> --
> 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 Fri Jul 07 2023 - 06:00:02 PDT
