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
> *$tleap -f leaprc.ff99SBildn*
> *source leaprc.gaff*
or
> *$tleap -f leaprc.ff99SBildn*
> *source leaprc.ff99SBildn*
Thank you once again for the support.
On Wed, Oct 9, 2013 at 8:50 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Wed, Oct 9, 2013 at 10:20 AM, Shomesankar Bhunia <
> rightclickatrighttime.gmail.com> wrote:
>
> > Dear Jason,
> > I would like to know one thing if I source leaprc.ff99SBildn, how i
> should
> > proceed
> > Is it like this? I have followed the amber tutorial
> > http://ambermd.org/tutorials/basic/tutorial4b/.
> >
> > should I also apply leaprc.ff99SBildn in case of ligand also?
> >
>
> leaprc.ff99SBildn is a protein force field. Organic ligands are typically
> parametrized with gaff (although it's important to note that gaff
> parameters may need to be fixed in some cases). A gaff-parametrized ligand
> is still compatible with ff99SBildn (and other related force fields, like
> ff99SB and ff12SB).
>
>
> >
> > tleap -f leaprc.ff99SBildn
> >
> > >source leaprc.gaff
> >
> > I am giving you the details.
> >
> > *for ligand*
> >
> >
> > antechamber -i sustiva_new.pdb -fi pdb -o sustiva.mol2 -fo mol2 -c bcc
> -s 2
> > parmchk -i sustiva.mol2 -f mol2 -o sustiva.frcmod
> > *$tleap -f leaprc.ff99SB*
> > *source leaprc.gaff*
> > SUS = loadmol2 sustiva.mol2
> > check SUS
> > loadamberparams sustiva.frcmod
> > saveoff SUS sus.lib
> > saveamberparm SUS sustiva.prmtop sustiva.inpcrd
> >
>
> The atom types in sustiva.mol2 are all gaff atom types (lower case), so
> there will never be any conflict with Amber atom types (which are all
> upper-case). The leaprc.gaff file is compatible with the Amber force field
> scripts (e.g., leaprc.ff99SB), so what you did here is fine (although for
> just the ligand, ff99SB is unnecessary).
>
> I'll also point out that you talk about using ff99SBildn at the top of this
> email, yet you are using ff99SB in your example scripts. These are
> different force fields...
>
> HTH,
> Jason
>
> P.S. Please don't send duplicate emails (especially within hours of sending
> the first). People will respond as they can (who the email is addressed to
> is typically not important).
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Oct 09 2013 - 09:00:03 PDT
