Just a comment to the input:
I guess, doing the solvent stripping after the imaging will result in a
huge increase of compute time, because every water molecule will be
imaged first and then deleted. Thus, I'd try to swap the two input lines.
Best,
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
Am 26.01.2024 um 06:20 schrieb Huang ZiJian via AMBER:
> Hi Enrico,
>
> The "center" and "autoimage" actions will modify coordinate information twice. Maybe the commands below would help:
>
> parm *.prmtop
> trajin *rod_*.nc 1 -1 10
> autoimage :374 # the residue near the center of the interface between the two prot.
> strip :WAT,Na+,Cl-
> trajout stripped_traj44.pdb
>
> Regards,
> Zijian
> ________________________________
> 发件人: Enrico Martinez via AMBER <amber.ambermd.org>
> 发送时间: 2024年1月26日 0:42
> 收件人: Steinbrecher, Thomas <thomas.steinbrecher.roche.com>; AMBER Mailing List <amber.ambermd.org>
> 主题: Re: [AMBER] [Sender Not Verified] cpptraj: post-threatment of the PBC for membrane system
>
> 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
>>>
>>> _______________________________________________
>>> 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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jan 26 2024 - 00:30:02 PST
