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 <jalem...@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 <jalem...@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
========================================
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