From: William Tao (ywtao.smu_at_gmail.com)
Date: Thu Mar 21 2019 - 21:27:42 CDT
Hi NAMD community,
I am recently trying to set up the QM/MM calculations with NAMD, especially
pure QM modeling of small molecules.
The issue I came across is that if I have the PDB coordinates of a small
molecule, e.g. methanol. Is there a quick way to generate "non-sense" PSF
files required by the QM/MM set-up? (As the MM force will be completely
discarded if we do pure QM simulation.)
If there is a way to do this, what kind of force field parameter file
should I provide? (Or any parameter file can be provided as it will no be
used...?)
Many thanks.
William
==
HETATM 1 O UNK 0 0.708 0.000 0.000 0.00 0.00
O
HETATM 2 C UNK 0 -0.708 0.000 0.000 0.00 0.00
C
HETATM 3 H UNK 0 -1.073 -0.769 0.685 0.00 0.00
H
HETATM 4 H UNK 0 -1.073 -0.195 -1.011 0.00 0.00
H
HETATM 5 H UNK 0 -1.063 0.979 0.331 0.00 0.00
H
HETATM 6 H UNK 0 0.994 -0.880 -0.298 0.00 0.00
H
END
==
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