VMD-L Mailing List

From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Wed Sep 02 2015 - 14:59:12 CDT

Hi Christopher,

Thank you so much for your help. Yes, I am using VMD 1.9.2, and I had
missed the "Analyze" button (does the tutorial have it?). Once I went
through that step, everything worked out fine. I did add the all36_cgenff
and all36_prot PAR files in the "Associated parameter files".

For my structure, I generated the pdb using Avogadro, loaded it into
Molefacture, and from that point just followed the tutorial. One question I
have is.......does all the non-bonded term have to be filled up before
doing the Gaussian Optimization? I am asking because one or two atoms in my
system are not exactly similar to the ones in the parameter files. For
these atoms, should I look for the most similar ones, or should I leave the
non-bonded part blank?

Also, how would I include impropers like you suggested?

Regards,
Chitrak.

On Wed, Sep 2, 2015 at 2:37 PM, Mayne, Christopher G <cmayne2_at_illinois.edu>
wrote:

> 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.
>
>