Hello,
Thanks for your so nice cooperation.
--indrajit
---------------------------------------------------------------------
Indrajit Deb
Kolkata, India.
Mob: +919239202278
On Tue, May 22, 2012 at 5:18 AM, David Condon <dec986.gmail.com> wrote:
> 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
> > >> > > > _______________________________________________
> > >> > > > AMBER mailing list
> > >> > > > AMBER.ambermd.org
> > >> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > >> > > >
> > >> > > _______________________________________________
> > >> > > AMBER mailing list
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> > >> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >> > >
> > >> > _______________________________________________
> > >> > AMBER mailing list
> > >> > AMBER.ambermd.org
> > >> > http://lists.ambermd.org/mailman/listinfo/amber
> > >> >
> > >>
> > >> _______________________________________________
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> > >> AMBER.ambermd.org
> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >>
> > >>
> > >
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> >
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Received on Tue May 22 2012 - 00:00:04 PDT
