Hello Thomas,
yes actually these 2 residues are located in the central part of the
system. I also did some tests and found that the issue (relocation of
the entire complex towards some part of the membrane) was resulted
from the autoimage commande of the cpptraj... Probably some further
modifications could be required.
Yours with thanks,
Enrico
Il giorno gio 25 gen 2024 alle ore 08:20 Steinbrecher, Thomas
<thomas.steinbrecher.roche.com> ha scritto:
>
> Hi Enrico,
>
> well, are residues 49 and 374 in the center of the box? Hard to say if anything in your input is wrong without knowing that. You dont seem to do anything to align the protein, so ptraj only centers on the position of these two residues.
>
> Kind Regards,
>
> Thomas
>
> On Wed, Jan 24, 2024 at 5:53 PM Enrico Martinez via AMBER <amber.ambermd.org> wrote:
>>
>> **Warning** The sender address (Enrico Martinez via AMBER ) can not be verified, sender email address could be spoofed. Please take care to proceed.
>> Dear Amber community !
>>
>> I have another question related to post-treatment of MD trajectory
>> with membrane system.
>>
>> This time dealing with the modeling of dimeric GPCR (fully embedded in
>> the membrane) I use the following script to remove PBC from the
>> trajectory.
>>
>> parm *.prmtop
>> trajin *rod_*.nc 1 -1 10
>> trajout stripped_traj44.pdb
>> strip :WAT,Na+,Cl-
>> center :49,374 # center on the 2 residues involved in the prot-prot contact
>> autoimage
>>
>> Briefly, it does everything correctly (no jumps across the pbs etc)
>> but the both proteins look a bit shifted (although I have tried to
>> center the view in my cpptraj script) towards one of the parts of the
>> membrane (please see the screenshot attached !). Would it be rather
>> possible to orient the protomers in order that it could be perfectly
>> in the center plane ?
>>
>> Many thanks in advance !
>>
>> Sincerely
>>
>> 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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Received on Thu Jan 25 2024 - 09:00:02 PST
