VMD-L Mailing List

From: Mohan maruthi sena (maruthi.sena_at_gmail.com)
Date: Tue Mar 08 2016 - 05:11:53 CST

Hello Sir,
                I am considering initial values of k and bo (equilibrium
bond length) as 0. In the article titled " Rapid Parametrization of Small
Molecules using the Force Field Toolkit", it is mentioned that initial
guess for bond and angle term needs to supply as input but I took 0. If I
mention initial guess values, I could generate non-zero k and b values. The
hessian calculations are terminated normally.

Thank you very much for a reply,

Regards,
Mohan

On Tue, Mar 8, 2016 at 12:00 AM, Mayne, Christopher G <cmayne2_at_illinois.edu>
wrote:

> Mohan,
>
> Indeed, these results look strange. Based on this information alone, it
> is impossible to know what the issue is. Double check the vdW terms
> (contained within the Additional Associated Parameter Files”), the
> optimized geometry that you’re inputing as “PDB File”, check that the
> hessian calculation terminated normally. You might also run the
> optimization with the “Write debugging log” turned on, and look through the
> output.
>
> Regards,
> Christopher Mayne
>
> > On Mar 3, 2016, at 11:32 AM, Mohan maruthi sena <maruthi.sena_at_gmail.com>
> wrote:
> >
> > Dear vmd users,
> >
> > I am using the fftk toolkit to generate parameters
> for my molecule. I have optimized the molecule and performed hessian
> calculations. When I am trying to generate bond parameters, the equilibrium
> bond length and K (force constant) values obtained are as shown below:
> >
> >
> > !atom type Kb b0
> > !
> > C C4 0.739 -0.001
> > C C2 0.153 0.000
> >
> > I could not understand why the values are too low. The initial parameter
> file contains 0 values are Kb abd b0. Could please suggest some of the
> possible reasons for the observed weird values for Kb and bo.
> >
> > Thank your very much for a reply in advance
> >
> >
> >
> > Regards,
> > Mohan Maruthi
>
> 

-- 
Thanks and Regards,
Mohan Maruthi