AMBER Archive (2006)

Subject: Re: AMBER: Combine amber-force field and gaff94 for one molecule?

From: Fenghui Fan (fenghui_fan_at_yahoo.com)
Date: Sun Nov 05 2006 - 14:13:57 CST

Please read
http://216.109.125.130/search/cache?p=Amber+DNA-Drug&fr=yfp-t-421&toggle=1&ei=UTF-8&u=www2.umdnj.edu/%257Ekerrigje/pdf_files/AMBER8_drug_dna.pdf&w=amber+dna+drug&d=HjMJT5IFNgYu&icp=1&.intl=us.

Why you do not choose this method?

Best regards.

Fenghui Fan

--- "M. L. Dodson" <mldodson_at_houston.rr.com> wrote:

> On Sunday 05 November 2006 11:45, Michel Becker
> wrote:
> > Dear AMBER users
> >
> > I would like to perform a MD with a covalently
> bound DNA-drug complex.
> > amber 7 and 8 is available.
> >
> > For the DNA I will use the AMBER force field but I
> would like to employ
> > simultaneously the gaff force field for the drug.
> >
> > Therefore, one bond, four angles and a few
> dihedral angles at the
> > connection between both residues will exhibit
> amber atom types as well as
> > gaff atom types.
> >
> > Does any complications result from that
> circumstance?
> >
> >
> >
> > Best regards
> >
> > Michel Beacker?
> >
> >
> >
> > Erweitern Sie FreeMail zu einem noch
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> > Mehr Infos unter
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> >
> [http://freemail.web.de/home/landingpad/?mc=021131]
>
> Here is the way I do this kind of simulation. I am
> assuming that
> the drug is bound covalently to a base. You will
> have to remove
> atoms from the normal base and the drug at the sites
> of the
> drug-base bond so that valence of all species can be
> satisfied.
> Create a new residue definition for a nucleotide
> from the cognate
> normal nucleotide, but without the atom removed at
> the site of the
> covalent bond. The sum of charges will not be zero.
> Create a new
> residue definition for your drug, but when you come
> to the resp
> charge fitting step, fix the charge of the atom
> removed (to
> satisfy valences) from the drug to be zero and the
> charge for the
> rest of the drug to equal the charge of the atom you
> removed from
> the base. Edit the new drug residue definition to
> remove the atom
> at the drug site bonded to the base. The sum of
> charges will not
> be zero. However, after you combine things in LEaP,
> you will have
> a charge neutral system. Use the 'bond' command in
> LEaP to form
> the covalent bond between the drug and the base
> before you write
> the prmtop file. This is done in exactly the same
> way you create
> a disulfide bond in a protein.
>
> This procedure assumes no change in charge
> distribution of the
> base between the normal DNA nucleoside and that in
> the adducted
> DNA. This is certainly not correct in detail, but
> probably is a
> reasonable approximation for many kinds of studies.
> If you do not
> want to make that assumption, you must create a new
> residue from
> the drug PLUS the adducted base already bonded.
> This will mean a
> much larger QM calculation to get the charges, and
> will involve
> many more degrees of freedom for the conformation of
> the new
> residue, probably necessitating a multi
> conformational resp charge
> fit. I suggest you use RED if you want to do things
> this way.
> (Actually I would use RED, with or without
> antechamber, for both
> approaches). See the list archives for the URLs and
> discussions
> of new residue definition.
> --
> M. L. Dodson
> Email: mldodson-at-houston-dot-rr-dot-com
> Phone: eight_three_two-56_three-386_one
>
>
>
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