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
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.
Please mention if anything else is required for generating topology and
coordinate files.
Also are there any other points I have to keep in mind during energy
minimization and equilibration?
With regards,
Saikat
--
Saikat Dutta Chowdhury
Email: pbr322.dutta.gmail.com
Mob:
8017650842
9681144106
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Received on Tue Mar 17 2015 - 04:00:04 PDT
