[gmx-users] Re: Alternative TRP residue

[Justin A. Lemkul]

abelius wrote:
> Since the charges / bond lengths and angles were obtained for QM 
> calculations for the excited state of TRP I'm wondering if it would make 
> sense to apply the alternative bond lengths and keep the force constants 
> of TRP in the ground state?

I guess it's really going to depend on whether or not any of the bonded 
interactions are altered by this excited state.  If, for example, your excited 
state changes the bond order of a particular bond (i.e., promotion of an 
electron in a bonded orbital to one in an antibonding orbital), then I would 
argue that the force constants in the force field are incorrect, since that bond 
would thus be weakened.

-Justin

> Cheers,
> Abel
> 
> Justin A. Lemkul wrote:
>>
>>
>> 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
>>>>
>>>>
>>>
>>>
>>
> 
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-- 
========================================

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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