On 14/05/14 09:44, James Starlight wrote:
> Question regarding intal system preparation: for instance I have pdb
> consisted of GFP with chromophore and I'd like to perform qm_mm simulation
> of this protein treating chromophore by semi-empirical approximation and
> rest of the protein (+ solvent) using mm. How I should prepare initial
> prmtop of my GFP using tleap if I lack for the parameters for chromophore
> (wich are actualy will not be usefull during my qm-mm run) ?
With reference to GFP chromophore parameters, the supporting information
in this paper *may* be of use:
"Analytical Harmonic Vibrational Frequencies for the Green Fluorescent
Protein Computed with ONIOM: Chromophore Mode Character and Its Response
to Environment"
http://dx.doi.org/10.1021/ct400664p
Regards,
Mark
--
Mark J. Williamson
Unilever Centre for Molecular Informatics
Department of Chemistry
Lensfield Road
Cambridge CB2 1EW
http://www-ucc.ch.cam.ac.uk/members/mw529
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Received on Wed May 14 2014 - 02:30:03 PDT
