Dear Jason,
You are right I used the first one
>>*$tleap -f leaprc.ff99SBildn*
> > *source leaprc.gaff*
Thanks once again.
On Wed, Oct 9, 2013 at 9:15 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Wed, Oct 9, 2013 at 11:34 AM, Shomesankar Bhunia <
> rightclickatrighttime.gmail.com> wrote:
>
> > Dear Jason,
> > Thank you very much. I previously used ff99SB and while running MD i
> found
> > a shift in the protein backbone and in sidechains where two Ile units are
> > connected. Now I will be using ff99SBildn for the protein, but i have a
> > confusion for the protein while using ff99SBildn what should i do
> >
> > > *$tleap -f leaprc.ff99SBildn*
> > > *source leaprc.gaff*
> >
>
> This will load both the ff99SBildn and gaff force fields. If you have an
> organic ligand in your system, you should use this command.
>
>
> >
> >
> > or
> >
> > > *$tleap -f leaprc.ff99SBildn*
> > > *source leaprc.ff99SBildn*
> >
>
> This is redundant. The "-f" flag is the same as the "source" command. If
> you have an organic ligand, then you will not have any of the gaff
> parameters available to build the prmtop. This is OK as long as you
> printed every parameter to the frcmod file (but I don't think you did).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Wed Oct 09 2013 - 09:30:04 PDT
