[gmx-users] GFP chromophore topology help

[Ramachandran G]

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?

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
>
> ========================================
> --
> gmx-users mailing list    gmx-users at gromacs.org
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