Hi,
On Wed, Mar 9, 2022 at 1:04 AM Anita Meena
<Anita.Meena.cys20.chemistry.iitd.ac.in> wrote:
> I am trying to perform QM/MM calculations for protein ligand system
> using the tutorial
> https://www.bonvinlab.org/education/biomolecular-simulations-018/CPMD_tutorial/
This link appears to be broken.
> I have generated the eq_density.rst file successfully. When I visualized
> the eq_density.rst in VMD, I couldn't find the box (orthorhombic) I
> created.
Without seeing the tutorial we need more details about what you
actually did. Is this a solvated system? Did you add a box via e.g.
the solvatebox command in LEaP?
> However, now I want to move to CPMD in order to perform a QM/MM MD
> simulation, and CPMD does not apply “automatically” PBC to the starting
> configuration.
Again, it's hard to say what you are trying to do here. If your QM/MM
system doesn't already have a box/solvent, you would need to add them
via e.g. LEaP.
> Consequently, I need to “reimage” the coordinates into
> the primary unit cell. This task can be performed by the cpptraj
> program.
For imaging to work (with any program) your system needs to have a
unit cell (box) set up.
Can you provide more details about your system, and the exact steps
you've taken so far?
-Dan
> The tutorial suggests to Move the topology and final coordinates files
> to a folder and then create the input file eq_density.cpptraj for
> cpptraj with the command:
>
> cpptraj complex_solv.top < eq_density.cpptraj
>
> The command is using eq_density.cpptraj as an input, but I don't have
> this file.
>
> Right after this command the tutorial uses VMD to visualize
> reimaged.rst. But I don't know how this file has been generated using
> cpptraj and eq_density.cpptraj.
>
> It would be great if you can help me generating two files a)
> eq_density.cpptraj b) reimaged.rst
>
> Many thanks for your time and consideration.
>
>
> Sincerely,
> Anita
>
> -------- Original Message --------
> Subject: Re: [AMBER] [Amber]Not able to generate eq_density.cpptraj file
> while doing QM/MM calculations
> Date: 08.03.2022 18:36
> From: David A Case <david.case.rutgers.edu>
> To: AMBER Mailing List <amber.ambermd.org>
>
> On Tue, Mar 08, 2022, Anita Meena wrote:
>
> > I am trying to doing QM/MM calculation for protein-ligand complex. But
> > when i am using
> > cpptraj complex_solv.top < eq_density.cpptraj
> > command for preparing the MM files for CPMD , i am not able to
> > generate/write the eq_density.cpptraj.
>
> Can you (a) post what is in the "eq_density.cpptraj" file, which you are
> using as input to cpptraj? (b) Copy and paste the exact error message
> you
> are getting?
>
> Your command above uses eq_density.cpptraj as an input file, so you
> would
> not expect to "generate/write" it.
>
> ...thanks...dac
>
>
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Received on Wed Mar 09 2022 - 10:00:02 PST
