VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Wed Sep 02 2015 - 13:37:26 CDT

Chitrak,

I need a little bit more information in order to attempt to answer your questions.

1) Are you using VMD 1.9.2?
2) Are you including any "Associated Parameter Files"?

In 1.9.2 we updated the process of building the initial PAR file, which includes a step to analyze the input molecule, cross-checking against the associated parameter files, and to visually inspect the missing parameters. When you click the "Analyze" button, the boxes just below should populate with only the missing parameters, which can be written out to file via the "Write Initial Parameter File" button just below that. Upon analysis, do any of the boxes populate with missing parameters?

With regard to unnatural amino acids...
I would treat the ends in the same manner that you anticipate using the amino acid in production simulations. i.e., if you are going to use the amino acid as a single small molecule, I would use charged ends; if the amino acid will appear in the middle of a peptide/protein, then I would apply standard types of patches for termini. I very much doubt that a protonated carboxylic acid is what you want. Furthermore, I would attempt to leave as much of the original amino acid parameters in tact, i.e., and only refine the portions that you have modified. I don't know how you have constructed your PSF/PDB input, but make sure that you include any required impropers.

Regards,
Christopher Mayne

On Sep 2, 2015, at 11:05 AM, Chitrak Gupta wrote:

> Hi!
>
> I am new to the FFTK plugin. I have followed the steps of the tutorial video to generate the initial psf file (and that has all the information). However, when I use it to generate the initial par file, none of the bond/angles etc are defined. It is essentially an empty file. I am copy-pasting the part of the par file below.
>
> I also have an additional question. I am trying to parameterize an unnatural amino acid. To make the molecule "complete", I have a -COOH as the backbone carbonyl, I have two HN atoms attached to the backbone N, etc. Would these make the parameterization inaccurate?
>
>
> Here is my initial par file
>
> BONDS
> !V(bond) = Kb(b - b0)**2
> !
> !Kb: kcal/mole/A**2
> !b0: A
> !
> !atom type Kb b0
> !
>
> ANGLES
> !
> !V(angle) = Ktheta(Theta - Theta0)**2
> !
> !V(Urey-Bradley) = Kub(S - S0)**2
> !
> !Ktheta: kcal/mole/rad**2
> !Theta0: degrees
> !Kub: kcal/mole/A**2 (Urey-Bradley)
> !S0: A
> !
> !atom types Ktheta Theta0 Kub S0
> !
> !
>
> DIHEDRALS
> !
> !V(dihedral) = Kchi(1 + cos(n(chi) - delta))
> !
> !Kchi: kcal/mole
> !n: multiplicity
> !delta: degrees
> !
> !atom types Kchi n delta
> !
>
> IMPROPER
> !
> !V(improper) = Kpsi(psi - psi0)**2
> !
> !Kpsi: kcal/mole/rad**2
> !psi0: degrees
> !note that the second column of numbers (0) is ignored
> !
> !atom types Kpsi psi0
> !
>
> NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch -
> cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5
> !
> !V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
> !
> !epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
> !Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
> !
> !atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4
> !
>
> END
>
>
>
>
> Regards,
> Chitrak.