Hi, thanks for your time.
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/
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.
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. Consequently, I need to “reimage” the coordinates into
the primary unit cell. This task can be performed by the cpptraj
program.
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 Tue Mar 08 2022 - 22:30:02 PST
