Re: [AMBER] GFP Chromophore 1EMB.pdb,

From: FyD <fyd.q4md-forcefieldtools.org>
Date: Thu, 16 Feb 2012 14:43:02 +0100

Dear Yasuo Kurita,

You need to create a new force field library for molecular fragment(s)
corresponding to your chromophore
(http://www.cryst.bbk.ac.uk/PPS2/projects/jonda/chromoph.htm ?). You
could use the R.E.D. III.x tools or R.E.D. Server available .
http://q4md-forcefieldtools.org/ to do that.

Tutorials are also available at http://q4md-forcefieldtools.org/Tutorial/
See for instance:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#25
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#24

regards, Francois


> Dear Sirs
> This is Yasuo Kurita,a research scientist,in Physics Department of
> Tokyo University of Science.
> Thank you very much for your kind collaboration in advance.
> I am trying to make an equilibrium calculation of 1EMB.pdb for
> preparing Gaussian09 code
> "SAC-CI ONIOM" calculation of GFP chromophore to get a light
> emitting spectra.
> The Residue type of chromophore is CRO which is not a standard Amino
> acid residue.
> So "saveamberparm" command reject to make the top and res files.
> Could you let me know how I can solve this problem?
> I am very sorry to bothering you so much.
> Your kind suggestion would be very much appreciated.
> Thank you very much and best regards
> Y.Kurita



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Received on Thu Feb 16 2012 - 06:00:03 PST
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