[gmx-users] Re: Alternative TRP residue

[Justin A. Lemkul]

abelius wrote:
> 
> But How can I determine this constant? (I guess using the one of normal 
> TRP would make no sense)

I would suggest reading the primary literature for your force field of interest. 
  How did the original authors assign these parameters?  Usually bonded 
information comes from experimental data (spectroscopy, etc.)

-Justin

> Thanks,
> Abel
> 
> 
> 
> Justin A. Lemkul wrote:
>>
>>
>> abelius wrote:
>>> Thank you for your reply,
>>>
>>> I was just struggling to get the ffxxxbon.rtp syntax right since I 
>>> only have atom distances to create the bonds.
>>> So can anyone tell me what the correct syntax is for these defines in 
>>> the ffxxxbon.rtp file?
>>>
>>> #define <name> <distance in nm?> <?>
>>>
>>
>> ? = force constant
>>
>>> Furthermore where and how can I add the angle information?
>>>
>>
>> Angles are defined similarly
>>
>> #define <name> <equilibrium angle> <force constant>
>>
>> -Justin
>>
>>> Thanks,
>>> Abel
>>>
>>>
>>> Gerrit Groenhof wrote:
>>>> You can use #define's
>>>>
>>>> Like
>>>> [ bonds ]
>>>> C1 C2 e_c1c2
>>>>
>>>> Then in the ffxxxbon.rtp
>>>>  you define these things explicitly
>>>>
>>>> #define e_c1c2 0.15 123445
>>>>
>>>> Gerrit
>>
>>
> 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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