Thank you Carlos for the suggestion.
On Wed, Mar 18, 2015 at 3:46 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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--
Saikat Dutta Chowdhury
Email: pbr322.dutta.gmail.com
Mob:
8017650842
9681144106
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Received on Thu Mar 19 2015 - 01:30:02 PDT
