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 - 09:00:05 PDT
