Hi Indrajit,
The residue library file was generated here in the Turner lab.
-Dave
On Mon, May 21, 2012 at 6:17 PM, Indrajit Deb <biky2004indra.gmail.com>wrote:
> Hi,
>
> I also got the 1.frcmod.parmCEZ.parmbsc.parmBETA from Yildirim 2012 paper
> (supporting material). Will you please let know where did you got the
> 2. *residues.parmCEZ.parmbsc.lib
> file.
>
> Thanks
>
> --indrajit
> *
>
>
>
> ---------------------------------------------------------------------
> Indrajit Deb
> Kolkata, India.
> Mob: +919239202278
>
>
> On Tue, May 22, 2012 at 3:36 AM, Indrajit Deb <biky2004indra.gmail.com
> >wrote:
>
> > Got it. Thanks for your help.
> >
> >
> >
> >
> >
> > ---------------------------------------------------------------------
> > Indrajit Deb
> > Kolkata, India.
> > Mob: +919239202278
> >
> >
> > On Tue, May 22, 2012 at 3:34 AM, David Condon <dec986.gmail.com> wrote:
> >
> >> I renamed the residues file since gmail won't let me send anything
> ending
> >> in .lib.
> >>
> >> On Mon, May 21, 2012 at 5:43 PM, Indrajit Deb <biky2004indra.gmail.com
> >> >wrote:
> >>
> >> > Thank you very much. Can you please provide me the files:
> >> >
> >> > 1) frcmod.parmCEZ.parmbsc.parmBETA
> >> > 2) residues.parmCEZ.parmbsc.lib
> >> >
> >> > Thanks again.
> >> >
> >> > ---indrajit
> >> >
> >> >
> >> >
> >> > ---------------------------------------------------------------------
> >> > Indrajit Deb
> >> > Kolkata, India.
> >> > Mob: +919239202278
> >> >
> >> >
> >> > On Tue, May 22, 2012 at 2:51 AM, David Condon <dec986.gmail.com>
> wrote:
> >> >
> >> > > Hi Indrajit,
> >> > >
> >> > > Here is one tleap file I used to load the AMBER99Tor force field,
> >> where
> >> > it
> >> > > needs the files:
> >> > >
> >> > > 1) frcmod.parmCEZ.parmbsc.parmBETA
> >> > > 2) residues.parmCEZ.parmbsc.lib
> >> > > 3) some pdb (here caau.s.syn.pdb)
> >> > >
> >> > > source oldff/leaprc.rna.ff99
> >> > > > addAtomTypes {
> >> > > > { "C1" "C" "sp2" }
> >> > > > { "C2" "C" "sp2" }
> >> > > > { "C3" "C" "sp2" }
> >> > > > { "C4" "C" "sp2" }
> >> > > > { "OZ" "O" "sp2" }
> >> > > > { "CI" "C" "sp2" }
> >> > > > }
> >> > > > loadamberparams frcmod.parmCEZ.parmbsc.parmBETA
> >> > > > loadoff residues.parmCEZ.parmbsc.lib
> >> > > > mol = loadpdb caau.s.syn.pdb
> >> > > > addions mol Na+ 0
> >> > > > solvateoct mol TIP3PBOX 8.65
> >> > > > saveamberparm mol prmtop inpcrd
> >> > > > quit
> >> > > >
> >> > >
> >> > > Does this help?
> >> > > -Dave
> >> > >
> >> > > On Mon, May 21, 2012 at 4:21 PM, Indrajit Deb <
> >> biky2004indra.gmail.com
> >> > > >wrote:
> >> > >
> >> > > > Hi, AMBER users,
> >> > > >
> >> > > > Can anyone provide me the AMBER99TOR and AMBER99EZ force field and
> >> the
> >> > > > instruction how to load it in tLEAP ? AMBER12 does not provide
> these
> >> > > force
> >> > > > fields.
> >> > > >
> >> > > >
> >> > > > Thanks in advance.
> >> > > >
> >> > > >
> >> > > >
> >> > > >
> >> ---------------------------------------------------------------------
> >> > > > Indrajit Deb
> >> > > > Kolkata, India.
> >> > > > Mob: +919239202278
> >> > > > _______________________________________________
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> >> > > > AMBER.ambermd.org
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> >> > > >
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> >> > >
> >> > _______________________________________________
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> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >>
> >> _______________________________________________
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> >>
> >>
> >
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Received on Mon May 21 2012 - 17:00:03 PDT
