[gmx-users] GFP chromophore topology help

[Justin A. Lemkul]

Ramachandran G wrote:
> Thank you, Justin..
> 
> I added the all the needed connectivity for GFP chromophore in the
> aminoacid.rtp(mentioned -C and +N to indicate the preceding and
> following residue) and also defined the residue as "Protein" in
> residuetypes.dat. For the non existing bond types, bond angles, proper
> and improper dihedrals, i added newly in the file ffbonded.itp. Also
> hydrogen atom connectivity are defined in the .hdb file.
> 
> The structure looks perfect after pdb2gmx but when i do minimization,
> the atoms(N+ and C-) chromphore along with neighbouring residue
> terminals are flying apart. So i don't know where i am making
> mistakes.
> 
> Should i need to give information in the Termini database flie *.tdb ? or
> Is this due to wrong force constant values?  or
> Is my force field parameter has mistakes?
> 

The termini databases are not used for the Amber force fields.  If you're 
getting incorrect physical behavior, I'd suspect whatever parameters you're 
using are incorrect.

-Justin

> Thank your for you help.
> Rama
> 
> On Fri, Nov 12, 2010 at 6:20 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>
>> Ramachandran G wrote:
>>> Thank you for the help.
>>>       I have successfully constructed the chromphore molecule but
>>> still have problem in connecting it to the neigbhouring residues. I
>>> don't know how the connection sequence needs to be given in gromacs.
>>> Please help
>>>
>> You stand a much better chance of getting useful help if you at least
>> describe what you attempted and why it didn't work.  For the GFP
>> chromophore, which incorporates into the backbone, you need to add
>> connectivity in the .rtp file like any other amino acid residue (-C and +N),
>> and define the residue as "Protein" in residuetypes.dat (if using version
>> 4.5.x).  Without knowing what you've done, though, I'm only guessing.
>>
>> -Justin
>>
>>> with regards,
>>> Rama
>>>
>>> On Tue, Nov 9, 2010 at 3:22 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>>> Ramachandran G wrote:
>>>>> Dear gromacs users:
>>>>>
>>>>>       I have constructed the Amber03 force fields parameters
>>>>> (bonds,angles, proper and imporer dihedral.....) for the chromophore
>>>>> (p-hydroxybenzylidene-imidazolinone) inside GFP system and got the
>>>>> topology. But after energy minimization of the system, the
>>>>> conformation of the chromophore totally changed and the benzene and
>>>>> imidazole ring got puckered although i did not got any error message.
>>>>>
>>>> No Gromacs tool will check your work for you.  It will do what you tell
>>>> it.
>>>> Likely you omitted some necessary bonded parameters (bonds, angles,
>>>> impropers, etc).  Either that, or the parameters you supplied produce the
>>>> incorrect behavior.
>>>>
>>>> -Justin
>>>>
>>>>> Could anyone help me? Thank you.
>>>>>
>>>>>
>>>>> with regards,
>>>>> Rama
>>>> --
>>>> ========================================
>>>>
>>>> Justin A. Lemkul
>>>> Ph.D. Candidate
>>>> ICTAS Doctoral Scholar
>>>> MILES-IGERT Trainee
>>>> 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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>>>
>>>
>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> 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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> 

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

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

========================================