VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Mar 04 2021 - 09:39:23 CST

Yes, you should definitely use ffTK instead:
  http://www.ks.uiuc.edu/Research/vmd/plugins/fftk/

Best regards,
  John Stone

On Thu, Mar 04, 2021 at 02:48:11PM +0000, Mandayam Bharathi, Harsha wrote:
> Hi,
> I used "paratool" only. I typed paratool in the Tkconsole and the paratool
> ui was launched. That's what I ended up using. Do you suggest that I use
> ffTK instead? Thank you so much for your response.
> Thanks
> Harsha
>
> --------------------------------------------------------------------------
>
> From: John Stone <johns_at_ks.uiuc.edu>
> Sent: Wednesday, March 3, 2021 10:30 PM
> To: Mandayam Bharathi, Harsha <mandayambharathi.1_at_buckeyemail.osu.edu>
> Cc: vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
> Subject: Re: vmd-l: Redundant entries in force field parameters generated
> by paratool plugin in VMD
>
> Hi,
> You wrote "paratool", however I'm assuming you actually used FFTK,
> right?
> The old "paratool" plugin has been removed from visible VMD menus since it
> has been superceded by FFTK. I just want to ensure that the right people
> see your post, since nobody will be responding to inquiries about paratool
> since it has long since been replaced by FFTK.
>
> Best,
> John Stone
>
> On Wed, Mar 03, 2021 at 06:03:25PM +0000, Mandayam Bharathi, Harsha wrote:
> > Hello everyone,
> > I was attempting to parametrize Kanamycin A molecule using the
> paratool
> > plug-in in VMD 1.9.4. After the gaussian calculations were performed,
> this
> > plug-in was used to generate the kan_A.par file. The issue I am
> having is
> > that there are multiple values of force field parameters for the same
> kind
> > of bond, angle, dihedral, etc. For example, this is a section from
> the
> > parameter file that was generated:
> >
> > ! Parameters for components KAN
> >
> > ! To be used in combination with:
> >
> > ! par_all36_cgenff.prm
> >
> > ! par_all36_lipid.prm
> >
> > ! par_all36_na.prm
> >
> > ! par_all36_prot.prm
> >
> > BONDS
> >
> > !
> >
> > !V(bond) = Kb(b - b0)**2
> >
> > !
> >
> > !Kb: kcal/mole/A**2
> >
> > !b0: A
> >
> > !
> >
> > !atom type Kb b0
> >
> > !
> >
> > CG321 NTL 207.761 1.4942
> >
> > CG311 NTL 306.760 1.4719
> >
> > CG311 NTL 352.721 1.4618
> >
> > CG311 NTL 280.483 1.4903
> >
> > NTL HGP5 357.470 0.9998
> >
> > NTL HGP5 350.040 1.0003
> >
> > NTL HGP5 363.272 1.0001
> >
> > NTL HGP5 426.933 0.9997
> >
> > NTL HGP5 293.770 0.9995
> >
> > NTL HGP5 359.689 1.0001
> >
> > NTL HGP5 345.829 1.0000
> >
> > NTL HGP5 266.656 1.0000
> >
> > NTL HGP5 329.161 1.0000
> >
> > NTL HGP5 395.012 0.9999
> >
> > NTL HGP5 428.309 0.9994
> >
> > NTL HGP5 410.271 1.0001
> >
> > OG311 HN5 304.132 1.0001
> >
> > OG311 HN5 371.604 1.0004
> >
> > OG311 HN5 346.415 0.9999
> >
> > OG311 HN5 398.865 0.9998
> >
> > OG311 HN5 239.699 1.0000
> >
> > OG311 HN5 365.149 1.0003
> >
> > OG311 HN5 375.808 0.9997
> >
> > In the above example NTL HGP5 bond parameter has 12 different values.
> When
> > I use this file to run a NAMD simulation, it takes the last value by
> > default as it overwrites every time it finds an entry. The simulation
> is
> > running fine, but I am not sure if this is the correct way to do it.
> I
> > would really appreciate if anyone else who has faced similar issues,
> could
> > provide suggestions to find a way around this.
> >
> > Thanks
> >
> > Harsha
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
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> Phone: 217-244-3349
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>
> References
>
> Visible links
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-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/