I think you got your answers from the AMBER and GROMACS mailing list :)

Just a comment about PRODRG server, it is not the best choice for geometry optimization and charge calculation.

Lemkul, J.A., Allen, W.J., and Bevan, D.R. (2010) Practical Considerations for Building GROMOS-Compatible Small Molecule Topologies. J. Chem. Inf. Model. 50 (12): 2221-2235.

To our experience in the group it tends to define the "charge groups" inaccurately and produce optimized geometries that have out of plane hydrogens. There is a new online service for creating GROMOS compatible topologies for organic compounds:

http://compbio.biosci.uq.edu.au/atb/

It uses a knowledge-based approach and higher level QM calculations for geometry optimization and charge derivation. Yet the GROMOS ffs are united atom thus you lose in resolution.

If I had to chose an all-atom ff I would go for the AMBER99SB-ILDN for the protein and GAFF for the organic compound (your chromophore). Unless you have problems with the size of the organic molecule, you could optimize its geometry and calculate RESP charges using the R.E.D. server:

http://q4md-forcefieldtools.org/REDS/

Also check out the option "Use RED IV for automatically generating amino acid fragments " since your chromophore is covalently bonded to the protein (I never used it so I am not sure if this will do your job).


Thomas



On 30 January 2012 14:16, James Starlight <jmsstarlight@gmail.com> wrote:
Thomas,

It's a big protein with the some non-standart functional group like GFP

So the servers like PRORG are not good for that because of big size of the protein and subsiquent integration of both fragments.

James


2012/1/30 Thomas Evangelidis <tevang3@gmail.com>
Is it a small organic molecule or a modified amino acid within the context of a protein?



2012/1/29 Tim Schulte <tim.schulte@ki.se>
Dear James,
I agree with Joao, for fast and dirty minimisation you might try the program Chimera or VegaZZ. If you just wanna have an energy-minimized small molecule the Prodrg server is the way to go.
Cheers,
Tim

Von: Joćo Rodrigues [anaryin@gmail.com]
Gesendet: Freitag, 27. Januar 2012 09:56
Bis: James Starlight
Cc: pymol-users@lists.sourceforge.net
Betreff: Re: [PyMOL] Editing of the pdb structure

Dear James,

As someone has told you already, Pymol is a visualization tool, not a modelling suite. I guess you would be better off using something like AMBERTOOLS or MODELLER, depending on what you want to model, or any other "real" simulation/modelling package otherwise your results are very weak...

My opinion only.

Joćo [...] Rodrigues
http://nmr.chem.uu.nl/~joao



No dia 27 de Janeiro de 2012 09:50, James Starlight <jmsstarlight@gmail.com> escreveu:
Arne, Thomas

Thanks alot. Bond works finw


I'd like just to ask what about geometry optimisation of the new structure

E.g I want create 5memb imidazole ring where the 2 adj atoms are apart from 1.5 A from each other.

When I've create new bond by bond command new ring look like 6memb ( like benzol) because of long distance between adj atoms.

How I could optimise geometry of the new mollecule? Have pymol some built-in functions like conformational search be means of monte carlo or energy minimisation ?


James


2012/1/27 Thomas Holder <speleo3@users.sourceforge.net>
On 01/27/2012 09:11 AM, James Starlight wrote:
Dear PyMol users!

I need to create NEW covalent bond between two adjacent atoms. How this
could be done in PyMOl?

you could have guessed it: http://pymolwiki.org/index.php/Bond
:-)

The atoms must both be within the same object.


Cheers,
 Thomas

--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen


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

Thomas Evangelidis

PhD student

Biomedical Research Foundation, Academy of Athens

4 Soranou Ephessiou , 115 27 Athens, Greece

email: tevang@bioacademy.gr

          tevang3@gmail.com


website: https://sites.google.com/site/thomasevangelidishomepage/




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Thomas Evangelidis

PhD student

Biomedical Research Foundation, Academy of Athens

4 Soranou Ephessiou , 115 27 Athens, Greece

email: tevang@bioacademy.gr

          tevang3@gmail.com


website: https://sites.google.com/site/thomasevangelidishomepage/