Brent,
Many thanks for suggestions!
Also I wounder to know if some non-standard residues (for example hem) has
been already included in one of the existing amber's param sets ?
Best,
James
2014-05-11 16:35 GMT+04:00 Brent Krueger <kruegerb.hope.edu>:
> James,
>
> The general method described in TUTORIAL A1 Old: Building your own Custom
> Residues <http://ambermd.org/tutorials/advanced/tutorial1_orig/index.htm>
> is
> basically the same as described in the newer version Tutorial A1: Setting
> up a DNA-Ligand
> System<http://ambermd.org/tutorials/advanced/tutorial1/index.htm>
> . Both tell you how to set up a custom residue, so both should be helpful
> to you in that sense. The newer one has (we feel) a bit more detail about
> how to think about fragments as well as considerations regarding
> appropriate atomic charges; it is a fairly complicated custom residue
> scheme so it should prepare you reasonably well for any of your situations.
>
>
> Cheers,
> Brent
>
>
>
>
>
> On Sun, May 11, 2014 at 6:24 AM, James Starlight <jmsstarlight.gmail.com
> >wrote:
>
> > Thanks for suggestions!
> > I've noticed that TUTORIAL A1 Old: Building your own Custom
> > Residues<http://ambermd.org/tutorials/advanced/tutorial1_orig/index.htm
> > >was
> > marked as the old version so I thought that that method was out of
> > date
> > :)
> >
> >
> > James
> >
> >
> > 2014-05-08 15:17 GMT+04:00 Jason Swails <jason.swails.gmail.com>:
> >
> > > On Thu, 2014-05-08 at 10:43 +0400, James Starlight wrote:
> > > > Dear Amber users!
> > > >
> > > > I'm looking for some tutorial where I could find information about
> > > > inclusion of non-standard residues into the system using amber param
> > > sets.
> > > > For instance I need to simulate Rhodopsin which contain co-factor
> > retinal
> > > > covalently attached to the amino acid sequence of the protein.
> Another
> > > > intresting protein for me is GFP with the covalently bonded
> chromophore
> > > > merged both from N and C termi to the rest of the protein. What are
> the
> > > > general workflow of the construction of such systems ? Should I
> > > parametrize
> > > > non standard groups using Amber's CGenFF (or alternatively REDS
> > server)?
> > > > Could some one provide me with the script with the example of
> > integration
> > > > of such non-standard residues?
> > >
> > > Have you looked at the tutorial page? There is a tutorial for almost
> > > everything you say you want to do. http://ambermd.org/tutorials/ --
> you
> > > should familiarize yourself with the material on this page since it can
> > > probably answer many of your questions.
> > >
> > > Also, CGenFF is a CHARMM thing, standing for the Charmm GENeral Force
> > > Field. Amber has the General Amber Force Field (GAFF), and
> > > 'antechamber' is the program responsible for charge derivation and atom
> > > typing.
> > >
> > > R.E.D. is another option for more rigorous RESP-based charge
> derivation.
> > >
> > > HTH,
> > > Jason
> > >
> > > --
> > > Jason M. Swails
> > > BioMaPS,
> > > Rutgers University
> > > Postdoctoral Researcher
> > >
> > >
> > > _______________________________________________
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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> _______________________________________________
> Brent P. Krueger.....................phone: 616 395 7629
> Associate Professor................fax: 616 395 7118
> Hope College..........................Schaap Hall 2120
> Department of Chemistry
> Holland, MI 49423
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Received on Mon May 12 2014 - 00:30:03 PDT
