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From: Mandayam Bharathi, Harsha (mandayambharathi.1_at_buckeyemail.osu.edu)
Date: Wed Mar 03 2021 - 12:03:25 CST

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