Date: Fri, 7 Jul 2023 10:42:41 +0200
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
>>
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>> 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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(image/png attachment: rmsf.png)
