Subject: Summary: solvation algorithm

From: Renxiao Wang <[email-masked]>
Date: Wed, 31 Jan 2001 08:13:28 -0800 (PST)

Dear CCLers,

Last week I posted a query looking for algorithm/program for solvating 
molecules with explicit waters. Thanks for all the kind answers and here 
comes the summary.

This is my original post:

For some reasons we need to solvate organic molecules or even proteins
with explicit water molecules. Will anybody recommend a reliable algorithm
for doing this? It will be ideal if it is able to reproduce the 'real'
Please note that we prefer an algorithm rather than a certain program. It
is simply because we are writing programs in our approach. We certainly
know about some programs, such as AMBER and CHARMm, which can place waters
around a given molecule. But we are a little bit skeptical for what they
generate on the screen. 

And these are the answers we got:

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> From [email-masked]  Thu Jan 25 19:34:57 2001

Fragment potentials for waters in GAMESS will represent the first shell
well if you know how to distribute them. Prior sampling with MD simulation
with care in selection of snapshots. Gas-phase cluster can also be easily
optimized. 

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> From [email-masked]  Thu Jan 25 23:40:58 2001

Since you're aware of amber and charmm, I'm sure you're aware of gromacs
as well (http://md.chem.rug.nl/~gmx/online2.1.html).  You should use its
program genbox, with which you can add a layer of water molecules around
any given structure.  Alternatively, you could generate a box of solvent
around your molecule, and perform energy minimization and possibly
position restrained molecular dynamics (PR on your molecule, thus let the
waters relax around it). 

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> From [email-masked]  Fri Jan 26 01:02:09 2001

If this makes you skeptical, then try quantum mechanics or X-ray
crystallography instead. Writing a program in "your own approach" will
certainly not improve the result unless you use a better description than
molecular mechanics (i.e. quantum chemistry). 

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> From [email-masked]  Fri Jan 26 01:04:39 2001

I have started to study aqueous mineral species (usually ions).  I first
performed usual ab initio studies, up to the begining of the second
hydratation spheres, however ab initio caculations are virtually
impossible for second sphere (geometry optimisation cannot be reliable) 
Next step would be to parametrise a model with the ab initio result (and
actually validate it with ab initio results for other similar molecules or
clusters) because usual ab initio calculations cannot presently model
liquid solvent, neither actually temperature corrections (despite they
produce some). The only difficulty is in finding a reliable model for your
solvent (I cannot help you for that): then you would use the model for
molecular dynamics. All this is a classical approach. 

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> From [email-masked]  Fri Jan 26 02:48:31 2001

I am interested by the same topic and I would be interested to know the
answers. Could you forward me a resume? 

Myself, I intend to use Monte Carlo simulated annealing with potentials
fitted on Quantum Chemical calculations

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> From [email-masked]  Fri Jan 26 07:07:28 2001

I haven't "played" with it yet, but I just got a program called Agoa that
is supposed to do just that: (http://www.dqf.ufpe.br/~zaldini/agoa.html). 
You might want to talk to the developer of Agoa...he may even wish to
collaborate! 

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> From [email-masked]  Fri Jan 26 08:26:18 2001

I thought I'd send you a short note, just wondering what problems you may
have encountered with adding waters using CHARMm.  The standard way CHARMm
researchers do this, is to first 'solvate' around a protein, using
something like an 8A or 10A shell around all the surface residues, and
then do some equiliibration dynamics to allow the waters to 'adjust' to
the protein environment.  The waters used to make the beginning 'shell',
have been equilibrated (as bulk, just by themselves) using periodic
boundary conditions, and adjusting the water characteristics to reflect
experimental water values such as density and the O-O
radial-dist.function.  Boxes of this 'equilibrated' water are freely
available, and we as well as our customers, have used them with no
noticable problems.  What kind of situations have you encountered to make
you "skeptical " ? 

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> From [email-masked]  Fri Jan 26 18:31:32 2001

We have developed a model, named as EPIC, for this purpose. You may look
up our papers in J.Phys. Chem. and Ind. J. Chem. in 1998-2000 for this
purpose.  Currently we are extending it for larger number of water
molecules. Of course, what contitutes the "first layer" or "first shell"
is rather difficult to define.  We have been able to use EPIC structure
for ab initio studies.  The agreement for energies is reasobaly good.  For
example, we have studied thyamine..n H2O with n upto 20, formaimide with
upto 20 etc.  Please contact us for details if interested.
Thanks...Shridhar Gadre

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> From [email-masked]  Sat Jan 27 06:32:28 2001

I believe that you have not see my message at CCL, anuncing my AGOA
program, that I judge that may be usefull to you. Please, visit the HP at: 
http://www.dqf.ufpe.br/~zaldini/agoa.html. AGOA does not do simulation,
but it purpose hydration shells from QM - ESP.  If you get interested,
please, contact me. 

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Best wishes,

Renxiao Wang