AMBER Archive (2002)

Subject: RE: solvateOct

From: Kristina Furse (kristina.e.furse_at_vanderbilt.edu)
Date: Tue Nov 26 2002 - 16:51:52 CST

If anyone else tries to do this, I thought I'd mention for the record, I ended
up going with the first, more general protocol (details below)--two passes
through LEaP, then copied the box information from the first prmtop file to
the second (%FLAG BOX_DIMENSIONS section), and then used this second modified
prmtop with the first coordat (since both were 3pt water models and the first
one had the correct box info) for the calculation.

I initially tried the second, simpler way, but couldn't get it to work. I even
used an edited leaprc.ff99 where I went in and replaced any mention of T3P
with SPC. From this I would get SPC for the crystallographic water I had
included, but still got T3P for the additional box water. I took a look at
solvents.lib, and please correct me if I'm interpreting it wrong, but I think
WATBOX216 may be specific to TIP3P after all. The entry for WATBOX216 in
solvents.lib seems to have the TIP3P charges included in the
"!entry.SPC.unit.atoms table str name str type int typex int resx int
flags int seq int elmnt dbl chg" section, though I must admit I'm not
entirely sure what I'm looking at in the file...

Thanks for the help!

Kristina

>===== Original Message From amber_at_heimdal.compchem.ucsf.edu =====
>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
>==================================================================

****************************************************
Kristina E. Furse
Department of Chemistry
Center for Structural Biology
Vanderbilt University
email: kfurse_at_structbio.vanderbilt.edu