dear amber user,
thank you for your reply.
but i have used same leaprc file earlier with other protein and it created
the .prmtop and inpcrd file.
recently i have installed the amber12tools and amber12 in my ubuntu system
it runs the sander module but wont run the tleap module.
regards
roopali
On Tue, Dec 9, 2014 at 9:42 AM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> just want to correct, we used "ff14SBonlysc" with GB8 in this paper.
>
> Hai
>
> On Mon, Dec 8, 2014 at 7:39 AM, David A Case <case.biomaps.rutgers.edu>
> wrote:
> > On Mon, Dec 08, 2014, ROOPALI VERMA wrote:
> >>
> >> I am trying to create my prmtop and inpcrd file from tleap of amber12
> for
> >> that i have created leaprc file
> >>
> >> source leaprc.ff96
> >
> > My geuss is that the error is in the "source leaprc.ff96" step: this is
> not a
> > recommended ff, and its leaprc file is in the "oldff" directory. Hence,
> no
> > protein libraries were loaded. You should see the following line in your
> > output:
> >
> > Could not open file leaprc.ff96: not found
> >
> > [Developers: I'm thinking we should make this a fatal error, rather than
> just
> > a warning.]
> >
> > You should be *sure* that this is the forcefield you really want. It has
> > rather poor secondary structure preferences. I am aware of claims that
> > this can be somewhat ameliorated by combining it with certain GB models,
> but
> > am not (personally) fully convinced. You should also consider using
> ff14SB
> > plus igb=8:
> >
> > %A H. Nguyen
> > %A J. Maier
> > %A H. Huang
> > %A V. Perrone
> > %A C. Simmerling
> > %T Folding Simulations for Proteins with Diverse Topologies Are
> Accessible in
> > Days with a Physics-Based Force Field and Implicit Solvent
> > %J J. Am. Chem. Soc.
> > %V 136
> > %P 13959-13962
> > %D 2014
> >
> > ...good luck....dac
> >
> >
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Dec 09 2014 - 00:30:02 PST
