The fluorine in my case is covalently bound not ionic flouride so I don't think an ions ff will help.
Digging deeper it looks as if my problem may be because there are van der Waals parameters for fluorine in the last section of parm99.dat (loaded by leaprc.ff99SB) but not in param10.dat (loaded by leaprc.ff12SB). Where should these parameters now be loaded from?
Kevin Parkes
Dr K E B Parkes
Director Computational Chemistry & Structural Biology
Medivir AB
Tel +44 (0)1799 532102
Mob +44 (0)7920 053412
Fax +44 (0)1799 532101
> -----Original Message-----
> From: Lachele Foley (Lists) [mailto:lf.list.gmail.com]
> Sent: 11 June 2012 17:01
> To: AMBER Mailing List
> Subject: Re: [AMBER] FF12SB + GLYCAM_06h + Fluorine
>
> You probably need to load an ions ff, too. This is a slight
> change in behavior from previous. Basically, we tried to get
> rid of any loads that weren't absolutely necessary. The idea
> was to keep people from being unaware where their parameters
> were coming from. See the old leaprc for the ff's that were
> loaded previously.
>
> On Mon, Jun 11, 2012 at 10:18 AM, Kevin Parkes
> <Kevin.Parkes.medivir.com> wrote:
> > Hi,
> >
> > I am trying to repeat some calculations I previously ran
> with ff99SB / GLYCAM_06 in Amber 10 on a protein system
> containing a glcyosated residue (OLS) and a non-natural
> residue containing fluorine for which I previously built a
> library file. Some small modifications are required to
> adjust for the new atom naming in GLYCAM but otherwise all
> the components load into tleap without error. However
> addions and solvateoct appear not to recognise the fluorine
> atoms and report "using default radius 1.50" and
> saveamberparm fails altogether with the error "Could not find
> type: F".
> >
> > Any suggestions on the cause of this error?
> >
> > Many thanks
> >
> > Kevin Parkes
> >
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>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
>
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Received on Tue Jun 12 2012 - 04:00:03 PDT
