In general case following to the amber's "Simulating a Solvated Protein
that Contains Non-Standard Residues" tutorial I've found that I should
initially create prmtop for the isolated non-standart residue firstly. How
It could be done in my case assuming that I have pdb of my chromophore with
added hydrogens (excluding hydrogens for first C and last N atoms which
will be connected to the rest of the backbone)?
*James*
2014-05-14 13:12 GMT+04:00 Mark Williamson <mjw.mjw.name>:
> 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 - 03:30:02 PDT
