Can you please post the exact contents of the input file you are
giving to cpptraj. Also post any warnings or error messages produced.
Thanks,
-Dan
On Thu, Mar 10, 2022 at 2:20 AM Anita Meena
<Anita.Meena.cys20.chemistry.iitd.ac.in> wrote:
>
> Hi, Sorry for the inconvenience.
> please find the working link given here.
> https://www.bonvinlab.org/education/biomolecular-simulations-2018/CPMD_tutorial/
>
>
>
>
>
> -------- Original Message --------
> Subject: Re: [AMBER] [Amber]Not able to generate eq_density.cpptraj file
> while doing QM/MM calculations
> Date: 09.03.2022 23:10
> From: Daniel Roe <daniel.r.roe.gmail.com>
> To: AMBER Mailing List <amber.ambermd.org>
>
> 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 Thu Mar 10 2022 - 09:00:02 PST
