From: Marcelo C. R. Melo (melomcr_at_gmail.com)
Date: Sat Mar 23 2019 - 12:25:04 CDT
Hi William,
QwikMD has a way to do that, exactly to solve this problem. Just load your
molecule using QwikMD, go to "structure manipulation", then "Add
Topo+Param". You will find an option to create topologies for unknown
molecules. You just need to give the total charge of the molecule.
Best,
Marcelo
--- Marcelo Cardoso dos Reis Melo, PhD Postdoctoral Research Associate Luthey-Schulten Group University of Illinois at Urbana-Champaign crdsdsr2_at_illinois.edu +1 (217) 244-5983 On Thu, 21 Mar 2019 at 21:29, William Tao <ywtao.smu_at_gmail.com> wrote: > 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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