On Mon, Apr 01, 2024, Giorgos Lambrinidis via AMBER wrote:
>
>I have a peptide-ligand with 350 atoms. I run the antechamber to calculate
>charges (AM1 method) but it takes more than 10 hours on AMD 9 using only
>one CPU....
>Is there any way to run the sqm in parallel to save time?
First: if your ligand is a peptide (or even a modified peptide) using charges
and force field parameters from an Amber protein force field is likely to
give better results.
Second, (if you have not done so), turn off minimization, which may be taking
the bulk of time for a large molecule. See Note 7 on p. 320 of the Amber
2023 Reference Manual (it's in Section 16.2).
It is possible to run sqm in parallel by using the sqm.MPI executable. But
(as I remember) parallelization only extends to a few MPI threads, because
you still need to diagonalize the Fock matrix.
...dac
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Received on Mon Apr 01 2024 - 09:00:02 PDT
