Re: Fastest way to get PSF file for pure QM simulation?

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
> ==
>
>

This archive was generated by hypermail 2.1.6 : Wed Dec 04 2019 - 23:20:39 CST