[gmx-users] filling missing param values

[gromacs query]

Dear Justin,

Thanks this paper is quite explained and requires much detailed study
(sorry am escaping!)
As I have these two params missing, is there any tool that can help me in
this regard or may be some approximation method I may use?

thanks


On Thu, Jul 25, 2013 at 3:28 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/25/13 8:25 AM, gromacs query wrote:
>
>> Dear All,
>>
>> I am working on some molecule and I have defined atom types with OPLSaa
>> and
>> all atom types really exist in oplsaa and well chosen so no approximation
>> in choosing atom types. During grompp, I found there are dihedral param
>> missing. e.g.
>> N CT CT NT
>> N CT CT N3
>>
>> Is there any 'good' way of finding/assuming dihedral params for this? or I
>> should choose values of some nearby atom types?
>>
>>
> The OPLS dihedral fitting strategy is exceptionally well explained in the
> Kaminski 2001 paper (reference in Gromacs manual).
>
> -Justin
>
> --
> ==============================**====================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
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> jalemkul at outerbanks.umaryland.**edu <jalemkul at outerbanks.umaryland.edu> | (410)
> 706-7441
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