AMBER Archive (2008)

Subject: Re: AMBER: frcmod:attn needs revision

From: Junmei Wang (junmwang_at_gmail.com)
Date: Wed Aug 13 2008 - 11:45:11 CDT

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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