AMBER Archive (2008)

Subject: Re: AMBER: Atom types/parameters for chromene

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Wed Mar 05 2008 - 12:07:05 CST

Does this mean that ff99SB is les integrable with gaff than parm99 and parm94?
I am using gaff for non polymeric ligands and ff99SB for the protein as ff99SB
was suggested as (on averaging advantages and disadvantages) the best protein
ff.
Thanks
francesco pietra

--- Junmei Wang <junmwang_at_gmail.com> wrote:

> We used CM for non-aromatic double bond when we developed the parm99 force
> field. However, my recommendation is to use gaff for small molecules. You
> can safely use amber protein force fields and gaff together. You can even
> merge two force fields into one parameter file (such as gaff + parm99sb)
> without any conflict. As a matter of fact, gaff inherited all parameters
> when possible from parm99 and parm94.
>
> Best
>
> Junmei
>
> On Wed, Mar 5, 2008 at 3:34 AM, <anna.schrey_at_gmx.de> wrote:
>
> > Dear all
> >
> > I am parameterising a chromene unit. Antechamber suggests the CM atom type
> > for the non aromatic double bond, but I am not sure if this fits, epecially
> > because the bond angle parameter is missing.
> >
> > So my question - which atom types are the best to use for the non-aromatic
> > sp2 carbons in chromene, styrene, enol ethers, or isolated double bonds,
> and
> > where I can get the parameters?
> >
> > Best regards,
> >
> > Anna
> > --
> > Dr. Anna Katharina Schrey
> > Rungestr. 12
> > D-10179 Berlin
> >
> > GERMANY
> >
> > phone +49(0)30 275 601 92
> > mobile +49(0)174 18 65 323
> >
> > GMX startet ShortView.de. Hier findest Du Leute mit Deinen Interessen!
> > Jetzt dabei sein: http://www.shortview.de/?mc=sv_ext_mf_at_gmx
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