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
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Received on Wed Oct 09 2013 - 08:30:10 PDT
