AMBER Archive (2002)

Subject: Re: solvateOct

From: David A. Case (case_at_scripps.edu)
Date: Fri Nov 22 2002 - 20:31:03 CST

On Fri, Nov 22, 2002, Kristina Furse wrote:

> I'm using the following procedure from the LEaP manual to set up a truncated
> octahedron periodic box of SPC/E water:
>
> "The normal choice for a TIP3 _solvent_ UNIT is WATBOX216, which is a snapshot
> from a room-temperature equilibration for this model. If you want to solvate
> with other water models (say TIP4P), try the following: (a) solvate the system
> with WATBOX216, using the default TIP3 model; (b) use ambpdb to convert your
> prmtop file to Brookhaven for-mat; (c) restart LEaP, choose the TIP4P water
> model (instructions are in the Database chapter), then use loadPdb to bring
> back in the system you have created."
>
> Steps a-c went fine, but my question is how to get the box information back in
> once the system has been reloaded with SPC/E chosen as water model. I imagine
> if I were using a regular box, the setBox command would put the box back in
> without changing the system. Is there something comparable for solvateOct?
>

Two potential answers:

------------------------------------------------------------------------------
First: following the generic suggestions from the LEap manual outlined above:

Do the following: after you re-load the pdb file, issue a "setbox <unit>
centers" to tleap, followed by saveAmberParm.

Then, look at the last line in the coordinate (prmcrd) file you just made,
and edit so that it matches the last line in the file you created with the
TIP3 solvent using the solvateOct command. Then you should be fine.

(Note that (since SPC/E and TIP3 waters have the same number of points) that
the edited prmcrd file you get by this procedure should exactly match the
prmcrd file you originally created for TIP3 water; only the prmtop files are
different.)
-----------------------------------------------------------------------------

Second idea, exploiting the fact the SPC/E is also a three-point water model,
just like Tip3:

load the spc/e parameters (i.e. loadAmberParams frcmod.spce). Then solvate
with WATBOX216 (solvateOct <unit> WATBOX216 ....). Then continue as before.

There is nothing in WATBOX216 that distinguishes TIP3 from SPC/E: they
both have the same atoms and bonds. Hence, if you have the SPC/E parmeters
(from the loadAmberParams command), you will get SPC/E water.
-----------------------------------------------------------------------------

I agree that this is unnecessarily complicated. We have pre-equilibrated
boxes for Tip3, Tip4 and Pol3, but not for other combinations. The first
solution, above, is the more generic one: you could use that idea to create
a solvated simulation with TIP5P, for example. The second option is simpler,
and would work for SPC/E or other 3point water models.

..hope this helps...dac 

-- 

==================================================================
David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
==================================================================