Hey, thank you very much for this idea !
So the command should be added before or after autoimage ?
Could you give me some example based on my script e.g.
parm protein.prmtop
trajin prod.netcdf 1 -1 1
trajout stripped_traj2.pdb
strip :WAT,Na+,Cl-
autoimage
# added align based on the main-chain atoms
align ’.CA,C,O,N,H’
Yours with thanks
Enrico
Il giorno ven 2 feb 2024 alle ore 15:21 Saikat Pal
<saikatpaliitg.yahoo.com> ha scritto:
>
> Dear Enrico,
>
> You can use the align command (https://amberhub.chpc.utah.edu/align/) to visualize conformational changes in the trajectory.
>
>
> Thanks and Regards,
>
> Saikat Pal
>
>
>
>
> On Friday, 2 February, 2024 at 08:44:59 am GMT-5, Enrico Martinez via AMBER <amber.ambermd.org> wrote:
>
>
> Dear Amber users !
>
> I have one more question about correct post-treatment of MD trajectory
> to remove PBC artifacts using cpptraj. Here is my script :
>
> parm protein.prmtop
> trajin prod.netcdf 1 -1 1
> trajout stripped_traj2.pdb
> strip :WAT,Na+,Cl-
> autoimage
>
> Here are two questions :
>
> 1) How could I remove all translations/rotation of the system as the
> whole in order that the protein could remain in the fixed place in the
> produced multi model pbb with the aim that I could only concentrate on
> its conformational motions ?
>
> 2) Would it be possible to create a new processed trajectory (in pdb)
> in the reverse order compared to input netcdf file, in order that I
> could see "the molecular movie" from the end to beginning ?
>
> Many thanks in advance
>
> Enrico
>
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Received on Fri Feb 02 2024 - 06:30:02 PST
