Hi!
Thank you Carlos, David and François for your answers!
I had tried Tutorial_four, but unfortunately it stops short about how to
really compute charges for fragments (they are prepared out from the
tutorial and you simply need to copy them)
I will now go through the two tutorials proposed, though I don't have access
to RED for the time being.
Thanks again for your help!
Miguel
2007/9/30, FyD <fyd.q4md-forcefieldtools.org>:
>
> Quoting "David A. Case" <case.scripps.edu>:
>
> > On Sat, Sep 29, 2007, Carlos Simmerling wrote:
> >
> >> how about
> >> *Simulating a Solvated Protein that Contains Non-Standard Residues*
> >> http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_four/
> >
> > You might also look at:
> >
> > http://amber.scripps.edu/antechamber/example.html
> >
> > There is an example there of preparing a non-standard residue. (But we
> need
> > to make things simpler than they are now.)
>
> You might look at:
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php
> -I.3.2.3- Single- or multi-conformation multi-orientation RESP fits
> for the central fragment of new amino-acids
> -I.3.2.4- Multi-molecule multi-conformation multi-orientation RESP
> fits for terminal fragments of new amino-acids
>
> regards, Francois
>
>
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--
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Georges Brassens
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Received on Wed Oct 03 2007 - 06:07:04 PDT
