I would recommend our ff14SB rather than ff99SB-ildn. It has improvements
in many amino acids other than ildn. Our manuscript is in review now.
On Mar 18, 2015 2:47 AM, "Saikat Dutta chowdhury" <pbr322.dutta.gmail.com>
wrote:
> Thank you.
>
> On Tue, Mar 17, 2015 at 6:23 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
> > On Tue, 2015-03-17 at 16:01 +0530, Saikat Dutta chowdhury wrote:
> > > Hello Amber users,
> > >
> > > I am trying to do a MD simulation using ff99SB_ildn force field with
> > > TIP4P-Ew water model.
> > > To generate the prmtop and inpcrd files I used following:
> > >
> > >
> > >
> > > *#Building topology and coordinate file*source leaprc.ff99SBildn
> > >
> > > *loadamberparams frcmod.tip4pewloadamberparams frcmod.ionsjc_tip4pew*
> > > WAT = T4E
> >
> > The WAT = T4E line is unnecessary, I think (at least it had no effect
> > when I ran a quick test).
> >
> > >
> > > test = loadpdb test_wild_type.pdb
> > > #charge test
> > >
> > > addions test Cl- 0
> > >
> > > *solvateoct test TIP4PEWBOX 10.0*
> > >
> > > saveamberparm test test_wt_box.prmtop test_wt_box.inpcrd
> > > savepdb test test_wt_box.pdb
> > >
> > > quit
> > >
> > >
> > > My question is whether this is the way to incorporate the TIP4P-Ew
> model
> > or
> > > not.
> >
> > Looks OK to me.
> >
> > > Please mention if anything else is required for generating topology and
> > > coordinate files.
> >
> > Not specifically relating to using the TIP4PEw model. Chapter 3 section
> > 10 of the Amber manual walks through picking a solvent model.
> >
> > > Also are there any other points I have to keep in mind during energy
> > > minimization and equilibration?
> >
> > There's really nothing different between TIP4PEw and TIP3P in terms of
> > simulation protocol.
> >
> > HTH,
> > Jason
> >
> > --
> > Jason M. Swails
> > BioMaPS,
> > Rutgers University
> > Postdoctoral Researcher
> >
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Saikat Dutta Chowdhury
> Email: pbr322.dutta.gmail.com
> Mob:
> 8017650842
> 9681144106
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Received on Wed Mar 18 2015 - 03:30:03 PDT
