On Sunday 05 November 2006 14:13, Fenghui Fan wrote:
> 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
>
The posting described a covalently bound drug. See below.
The tutorial is for a noncovalent complex.
> --- "M. L. Dodson" <mldodson.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
> >
> > leistungsstärkeren E-Mail-Postfach!
> >
> > > Mehr Infos unter
> >
> > *http://freemail.web.de/home/landingpad/?mc=021131*
> >
> > [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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--
M. L. Dodson
Email: mldodson-at-houston-dot-rr-dot-com
Phone: eight_three_two-56_three-386_one
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Received on Wed Nov 08 2006 - 06:07:11 PST
