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

From: William Tao (ywtao.smu_at_gmail.com)
Date: Thu Mar 28 2019 - 11:43:29 CDT

Hi Joao,

Many thanks for your instructions.

At present, the topology issue seems to be solved, but another issue came
up when I hit the "prepare" button under the QM/MM tag.

Here is what I have done.
1) load up my PDB file under "Advanced Run" in QwikMD;
2) "Structure Manipulation", set my "MOL" residue to type "QM";
3) "Add Topo+Param", load up my "STR" file and set its type also to "QM";
4) close and reopen VMD;
5) repeat steps (1)-(2), and the "structure check" status turns green for
the "Topologies & Parameters"; [If I don't load up the "str" file, and use
only the generated QM topology, it remains red]
6) go back to QwikMD window, because I want to do pure QM simulation, I
clicked the QM/MM tag;
7) Set up the solvent as "vacuum", keep only the QMMM-Min protocol with no
restraints;
8) add one QM region and set up the "n Atoms";
9) set up the ORCA path and turn off point charges;
10) set up the save path and then click Prepare

I got the following error message in a pop-up window:
Error during structure preparation: Autopsf error
Error: failed on end of segment
MOLECULE DESTROYED BY FATAL ERROR! Use
resetpsf to start over.

Do you have any clue on solving this issue?

Many thanks!

Best regards,

William

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

Joao Ribeiro <jribeiro_at_ks.uiuc.edu> 于2019年3月25日周一 上午9:26写道:

> Hi William,
>
>
>
> So QwikMD checks the topology files that it has by default and the ones
> added by the user for known residues (residues are recognized by their
> name, independently of their atom composition). Did you, by any change,
> added a different topology molecule with a residue name MOL? You can check
> this on the window “Topology & Parameters Selection” window (“Add
> Topo+Param” button).
>
>
>
> Just to make it clear, if you added your topology (.rtf or .str) file to
> QwikMD in the Topology & Parameters Selection” window, you don’t
> need/should not to generate the fake topology for the QM simulation. The
> same topology is used to run MM, QM/MM or QM simulations. What matters is
> to have a topology to generate the psf.
>
>
>
> 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: *Sunday, March 24, 2019 at 1:37 PM
> *To: *Joao Ribeiro <jribeiro_at_ks.uiuc.edu>
> *Cc: *NAMD <namd-l_at_ks.uiuc.edu>
> *Subject: *Re: namd-l: Fastest way to get PSF file for pure QM simulation?
>
>
>
> 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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