VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Mar 03 2021 - 21:30:41 CST

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has been superceded by FFTK.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since it has long since been replaced by FFTK.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
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/