AMBER Archive (2007)

Subject: Re: AMBER: TIP5P questions

From: Thomas Cheatham III (tec3_at_utah.edu)
Date: Thu Sep 13 2007 - 14:14:25 CDT

> I am having the following question regarding TIP5P usage. I am comparing
> results of TIP5P and TIP3P water (trying) wrt DNA+ ligand simulation.
>
> When I use the following commands:
> 1. solvateoct co TIP3PBOX 8.0
> 2. solvateoct co TP5 8.0

Please see the LEaP instructions for solvateBox (page 66 of AMBER 9
manual) which discusses using other water models such as TIP5P.

In short, as there is no TIP5PBOX, LEaP creates a pseudo crystal of waters
around your solute and this is less dense leading to fewer waters. What
is stated in the manual is to first build with TIP3P, then create a
prmtop/inpcrd, from these create a PDB, then reload the PDB with the water
model switched to TIP5P (i.e. easiest is to edit the PDB to replace "WAT"
with TP5).

When using TIP5P, make sure you have loaded the frcmod,

  frcmod = loadamberparams frcmod.tip5p

After you have loaded the PDB, the manual states using the setBox command,
followed by hand editing of the box information in the prmtop/inpcrd to
match what it was in TIP3P.

Alternatively, you can "add" water but set the closeness so high that no
additional water is actually added (where "aa" is the name of your model):

solvateoct aa TP5 0.0 iso 1000

You still will likely have to alter the box size to prevent undue long
equilibration as that procedure leads to a larger box than was created
with TIP3P hydration.

> Additionally, has any studies been done on the effect of using TIP5P on
> nucleic acids- please share if you know of any?

No, but note that in my experience with Ewald, the TIP5P model is not
optimal as it completely misses the boat on ionic solvation free
energies... If I were to do such a comparison, I would consider the
Ewald-adapted water models (TIP4PEW and maybe TIP5PEW) instead and focus
most of my effort on TIP4PEW as this performs well. Finally, if I were to
start a comparison now, I would suggest the parmbsc0 force field for
DNA and use Smith & Dang ion parameters...

-- tec3
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