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.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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Received on Sun Aug 17 2008 - 06:07:12 PDT
