AMBER Archive (2008)

Subject: Re: AMBER: frcmod:attn needs revision

From: Junmei Wang (junmwang_at_gmail.com)
Date: Wed Aug 13 2008 - 14:34:50 CDT

It is H-C#C-S-H. "#" stands for triple bonds
Junmei

On Wed, Aug 13, 2008 at 11:55 AM, <moitrayee_at_mbu.iisc.ernet.in> wrote:

> Thanks a lot. I needed it badly for running the simulation. It would be
> great if
> you please let me know what model system you have used so that i can report
> it
> later.
>
> Best Regards
> Moitrayee
>
> > Hi, for this particular molecule, the current rules cannot
> > generate/calculate bond angle parameter for hs-sh-c1. I have performed ab
> > initio calculations using a model molecule C#C-SH at MP2/6-311+G* level.
> > Here is the parameter based on the QM calculations
> >
> > ANGLE H- S- C 29.898 95.989
> >
> > The bond angle was from the optimized structure and force constant was
> > calculated using the parmcal program (H-S: 1.3556, C-S: 1.6968 and H-S-C:
> > 95.9893).
> >
> > All the best
> >
> > Junmei
> >
> > On Tue, Aug 12, 2008 at 5:18 PM, <moitrayee_at_mbu.iisc.ernet.in> wrote:
> >
> >> Hi
> >> I have generated a .prep file for homocysteine and used parmchk to
> generate
> >> the
> >> missing parameters. The output .frcmod is given below:
> >> remark goes here
> >> MASS
> >>
> >> BOND
> >>
> >> ANGLE
> >> hs-sh-c1 0.000 0.000 ATTN, need revision
> >> c1-c3-n3 67.899 109.740 Calculated with empirical approach
> >> c1-c3-c 64.875 110.975 Calculated with empirical approach
> >>
> >> DIHE
> >>
> >> IMPROPER
> >>
> >> NONBON
> >>
> >> I want to do a MD simulation using this ligand. But i assume before that
> i
> >> have
> >> to assign values to hs-sh-c1. How do i do the manual parametrization?
> Any
> >> help
> >> regarding this would be highly appreciated.
> >> Looking eagerly forward for a response.
> >> Thanks a lot in advance.
> >>
> >> Best regards,
> >> Moitrayee Bhattacharyya
> >> Molecular Biophysics Unit
> >> Indian Institute of Science
> >> Bangalore
> >> India
> >>
> >>
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