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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Mar 17 2015 - 06:00:03 PDT
