[gmx-users] GFP chromophore topology help

[Justin A. Lemkul]

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
>>
>> ========================================
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the www interface
>> or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
> 
> 
> 

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

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

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