Subject: SUMMARY: Looking for a Code to Solvate Molecules

From: Wibke Sudholt <[email-masked]>
Date: Thu, 6 Apr 2000 10:45:36 +0200

Dear CCLers,

two people ask me to present a summary of the responses to my question, so I'll
do this with this email (answers are edited a little bit). Most people suggest
to use BOSS or a related program, which is a full Monte Carlo package. Since I
only need a "small tool", I decided to use the code of Marcel Swart, which
seems to fit to my needs very well (hopefully, you don't get too many inquiries
now that I sent it to the list, Marcel :-) ).

Many thanks to  Stephen A. Decker,
                Deepak Singh          for interest;
                Willem P. van Hoorn,
                Brian K. Peterson,
                Daniel Severance,
                Rick Venable,
                David van der Spoel,
                Marcel Swart          for providing answers!

(in order of appearance in my mailbox; hopefully, I didn't forget anyone)

Wibke Sudholt
Institute of Theoretical Chemistry
Heinrich-Heine-University
Duesseldorf, Germany
[email-masked]

----------  Original Question  ----------
Subject: CCL:Looking for a Code to Solvate Molecules
Date: Mon, 3 Apr 2000 14:59:00 +0200
From: Wibke Sudholt <[email-masked]>

Dear CCLers,

I am looking for a program (preferably freeware Fortran code) which is capable
of the following (or parts of it):
* reads in the xyz coordinates of a solute molecule and reads in the xyz
coordinates of an (arbitrary, not only water) solvent molecule
* generates xyz coordinates of a cubic box filled with the solute molecule
surrounded by some kind of random mixture of solvent molecules (needs not to
be equilibrated or may have some order left)
* controles the size of the system by density, box size, number of solvent
molecules etc.
I have checked the internet with no success, as most of such programs can only
handle water or need predefined boxes filled with solvent molecules (programs
which generate those would also be a help).

Is anybody out there aware of such a program and willing to share his/her
code/knowledge with me?

Thank you very much in advance for your help

Wibke Sudholt
Institute of Theoretical Chemistry
Heinrich-Heine-University
Duesseldorf, Germany
[email-masked]

----------  Answer Message 1  ----------
Subject: RE: Looking for a Code to Solvate Molecules
Date: Mon, 3 Apr 2000 15:42:08 +0100
From: [email-masked]

BOSS by WL Jorgensen can do (almost all of) what you want, is written in
F77, and is academic software:
http://zarbi.chem.yale.edu

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 Dr. Willem P van Hoorn     IPC 557       
 Computational Chemistry    Phone: +44-1304-648470
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----------  Answer Message 2  ----------
Subject: RE: Looking for a Code to Solvate Molecules
Date: Mon, 3 Apr 2000 10:59:00 -0400
From: "PETERSON,BRIAN K." <[email-masked]>

Hi Wibke.  While you may find a solvation code, you might want to look at
grand-canonical Monte Carlo codes.   While there are some efficiency
problems with high density GCMC, for just preparing reasonably equilibrated
systems for input into something else, they should work fine.  I use the
Cerius2 sorption module for this.  One GCMC code available on the web is
from Thanos Panagiotopoulos' group at:
http://thera.umd.edu/jerring/gcmc/overview/overview.htm .  

brian peterson
Air Products and Chemicals, Inc.

----------  Answer Message 3  ----------
Subject: RE: Looking for a Code to Solvate Molecules
Date: Mon, 3 Apr 2000 09:33:18 -0700
From: Daniel Severance <[email-masked]>

Hi,
   The BOSS program from Bill Jorgensen at Yale does just what you want.
You can specify
your own solvents, and can do 2-part mixtures at least.  You do have control
over the box size as well.
   It's not freeware, but he doesn't charge much for academic institutions.
He can answer more specifically, since I've never used the solvent mixture
options and thus haven't paid attention to any more recent changes he may
have made.
   His e-mail address is [email-masked]
   Good luck!
      Dan

----------  Answer Message 4  ----------
Subject: Re: CCL:Looking for a Code to Solvate Molecules
Date: Mon, 3 Apr 2000 13:38:57 -0400 (EDT)
From: Rick Venable <[email-masked]>

I have some CHARMM scripts I've developed for solvating within any
orthorhombic shape (square corners), which I can provide if you are
interested in them.  I've also recently developed generalized scripts
for adding ions to the resulting box, by replacing selected water
molecules. 

Rick Venable                  =====\     |=|    "Eschew Obfuscation"
FDA/CBER Biophysics Lab       |____/     |=|
Bethesda, MD  U.S.A.          |   \    / |=|  ( Not an official statement or
[email-masked]          |    \  /  |=|    position of the FDA; for that,
[email-masked]              \/   |=|    see   http://www.fda.gov  )

----------  Answer Message 5  ----------
Subject: solvate
Date: Tue, 4 Apr 2000 00:11:56 +0200 (CEST)
From: David van der Spoel <[email-masked]>

Such a program "genbox" comes with the GROMACS set:
http://md.chem.rug.nl/~gmx
(and probably with many other MD packages).

genbox supports rectangular and triclinic boxes (which basically means all
periodic boxes) as well as nonperiodic systems (solvent layer). The type
of solvent is determined by your input file, and can be any organic
molecule, or mixture thereof.

Groeten, David.
________________________________________________________________________
Dr. David van der Spoel		Biomedical center, Dept. of Biochemistry
s-mail:	Husargatan 3, Box 576,  75123 Uppsala, Sweden
e-mail: [email-masked]	www: http://zorn.bmc.uu.se/~spoel
phone:	46 18 471 4205		fax: 46 18 511 755
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

----------  Answer Message 6  ----------
Subject: Re: CCL:Looking for a Code to Solvate Molecules
Date: Tue, 4 Apr 2000 12:01:42 +0200
From: Marcel Swart <[email-masked]>

Hi Wibke,

I've written a program which does just what you want:
given a solvent molecule and a solute molecule,
you have several options to fill several boxes at random with any 
given number of solvents/solutes.

It is not on the Web yet, cuz I feel I have to improve a bit upon it,
incl. Online manual etc., but I'd be happy to give you the source code.

If you want, I can make a tar-file of the source code as it is now,
and send this to you.

Marcel.
-- 
------------------------------------------------
drs. Marcel Swart

Theoretical Chemistry (MSC)
Molecular Dynamics (GBB)

Rijksuniversiteit Groningen
Chemistry Department
Nijenborgh 4
9747 AG Groningen
The Netherlands

tel : +31 - (0)50 - 3634377
fax : +31 - (0)50 - 3634441

E-mail : [email-masked]
WWW: http://theochem.chem.rug.nl/~marcel/
------------------------------------------------