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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>
--
Saikat Dutta Chowdhury
Email: pbr322.dutta.gmail.com
Mob:
8017650842
9681144106
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Received on Wed Mar 18 2015 - 00:00:03 PDT
