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

From: William Tao (ywtao.smu_at_gmail.com)
Date: Sun Mar 24 2019 - 13:33:03 CDT

Hi Joao,

Thank you for your instructions.

However, in my case, the left side of the "Generating Missing QM Region
Topology" window is empty and the dropdown list of "select residue" is also
blank. I have loaded this molecule into the QwikMD in the very beginning.
Do you have an idea what might go wrong here?

Following is the link of my PDB file and stream file.
https://www.dropbox.com/s/y92d6lr8yddtzj4/vmd_test.zip?dl=0

Many thanks.

Best regards,

William

Joao Ribeiro <jribeiro_at_ks.uiuc.edu> 于2019年3月23日周六 下午6:53写道:

> Hi William,
>
>
>
> In “Generating Missing QM Region Topology” window, on the right side, in
> the “Generate Topology,” you will find a dropdown menu “Select Residue.”
> Select your residue, and then the topology will be generated. The
> documentation for the QM/MM interface in QwikMD is a little bit delayed,
> but it will come.
>
>
>
> But if you already have the topology, feed QwikMD with the topology that
> you pasted in your email (in the “Topology & Parameters Selection” window)
> and prepare the QM/MM simulation where your molecule is the QM region.
>
>
>
> I hope this helps.
>
>
>
> Best
>
>
>
> João
>
>
>
> ……………………………………………………...
> João Vieira Ribeiro
> Theoretical and Computational Biophysics Group
> Beckman Institute, University of Illinois
>
> http://www.ks.uiuc.edu/~jribeiro/
>
> jribeiro_at_illinois.edu
>
> +1 (217) 3005851
>
>
>
> *From: *<owner-namd-l_at_ks.uiuc.edu> on behalf of William Tao <
> ywtao.smu_at_gmail.com>
> *Reply-To: *<namd-l_at_ks.uiuc.edu>, William Tao <ywtao.smu_at_gmail.com>
> *Date: *Saturday, March 23, 2019 at 2:36 PM
> *To: *NAMD <namd-l_at_ks.uiuc.edu>
> *Subject: *Re: namd-l: Fastest way to get PSF file for pure QM simulation?
>
>
>
> Hi Marcelo,
>
>
>
> Thank you for pointing me to the right direction with QwikMD.
>
>
>
> I have now located the "Structure Maniputation" button in the "Advanced
> Run" label. Then I clicked the "Generate QM Region Topology" button after I
> clicked "Add Topo+Param" button, a new dialogue window popped up titled
> "Generating Missing QM Region Topology". However, it has no information on
> that, but the right text edit widget seems to be editable.
>
>
>
> Till this point, I got lost. Do you have any instructions on this part? I
> checked the user-guide of QwikMD and QM/MM tutorial, but didn't find
> description on this.
>
>
>
> Many thanks.
>
>
>
> Best regards,
>
>
>
> William
>
>
>
> Following are my PDB file and stream file.
>
>
>
> ==
>
> HETATM 1 O MOL 0 0.708 0.000 0.000 0.00 0.00
> O
>
> HETATM 2 C MOL 0 -0.708 0.000 0.000 0.00 0.00
> C
>
> HETATM 3 H1 MOL 0 -1.073 -0.769 0.685 0.00 0.00
> H
>
> HETATM 4 H2 MOL 0 -1.073 -0.195 -1.011 0.00 0.00
> H
>
> HETATM 5 H3 MOL 0 -1.063 0.979 0.331 0.00 0.00
> H
>
> HETATM 6 H4 MOL 0 0.994 -0.880 -0.298 0.00 0.00
> H
>
> ==
>
>
>
> ==
>
> * Toppar stream file generated by
>
> * CHARMM General Force Field (CGenFF) program version 2.2.0
>
> * For use with CGenFF version 4.0
>
> *
>
>
>
> read rtf card append
>
> * Topologies generated by
>
> * CHARMM General Force Field (CGenFF) program version 2.2.0
>
> *
>
> 36 1
>
>
>
> ! "penalty" is the highest penalty score of the associated parameters.
>
> ! Penalties lower than 10 indicate the analogy is fair; penalties between
> 10
>
> ! and 50 mean some basic validation is recommended; penalties higher than
>
> ! 50 indicate poor analogy and mandate extensive validation/optimization.
>
>
>
> RESI MOL 0.000 ! param penalty= 0.000 ; charge penalty= 0.000
>
> GROUP ! CHARGE CH_PENALTY
>
> ATOM O OG311 -0.650 ! 0.000
>
> ATOM C CG331 -0.040 ! 0.000
>
> ATOM H1 HGA3 0.090 ! 0.000
>
> ATOM H2 HGA3 0.090 ! 0.000
>
> ATOM H3 HGA3 0.090 ! 0.000
>
> ATOM H4 HGP1 0.420 ! 0.000
>
>
>
> BOND H2 C
>
> BOND H4 O
>
> BOND O C
>
> BOND C H3
>
> BOND C H1
>
>
>
> END
>
>
>
> read param card flex append
>
> * Parameters generated by analogy by
>
> * CHARMM General Force Field (CGenFF) program version 2.2.0
>
> *
>
>
>
> ! Penalties lower than 10 indicate the analogy is fair; penalties between
> 10
>
> ! and 50 mean some basic validation is recommended; penalties higher than
>
> ! 50 indicate poor analogy and mandate extensive validation/optimization.
>
>
>
> BONDS
>
>
>
> ANGLES
>
>
>
> DIHEDRALS
>
>
>
> IMPROPERS
>
>
>
> END
>
> RETURN
>
> ==
>
>
>
> Marcelo C. R. Melo <melomcr_at_gmail.com> 于2019年3月23日周六 下午12:25写道:
>
> 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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