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

From: Joao Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Sat Mar 23 2019 - 18:47:12 CDT

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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