AMBER Archive (2008)

Subject: Re: AMBER: frcmod:attn needs revision

From: moitrayee_at_mbu.iisc.ernet.in
Date: Wed Aug 13 2008 - 23:51:50 CDT

Thank you very much.
Best regards
Moitrayee

> 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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