Dear Collegues,
Thank you for amber package. It is nice to use it. But I have some question.
I think, that amber treat QM region in QMMM without using MD atom types. I
want to treat metal ions and ligands without using prmtop and topology files
for them. How to do that? Is it correct to use prmtop and topology files for
protein only for QMMM, when I calculate complex i.e. protein+metal+ligand?
QM use for GAF-prmtop file. For meny atoms (metals and in ligands) AMBER
field have no parameters. So I want to calculate such atoms directly using
QMMM. But sender needs prmtop file for the hole molecular complex:) How to
calculate QMMM directly without prmtop file for QM region?
Thank you in advance!
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Received on Tue Sep 02 2014 - 00:30:03 PDT
