Subject: summary: implicit solvation programs

From: "Zhou Feng" <[email-masked]>
Date: Thu, 26 Sep 1996 11:33:48 -0500

Dear ccl:

 I posted a message inquiring programs which can do implicit solvent model
while
performing energy minimization & molecular dynamics. Here is a summary of the
responses I have got.  Thanks to all who replied!

On Sep 23, 11:32am, Zhou Feng wrote:
> Subject: CCL:(no subject)
> Hi:
>
>  I am looking for a reasonably accurate implicit solvation energy program
which
> can do some simple energy minimization or low temperature MD to predict the
> energies of a biomoleular system, there are moderate conformational changes
> which has to be predicted along with the energies. IS there anyone who can
give
> me some suggestions?  We have CHARMM & Delphi, but we need to do some
dynamics
> with the implicit solvent model.

MacroModel/BatchMin has GB/SA solvation, which will probably do what you need.
See the URL below for info. on cost and availability, and also for
literature references to GB/SA.

      -P.

--
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* Peter S. Shenkin, Chemistry, Columbia U., 3000 Broadway, Mail Code 3153,*
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From: "Robert Fraczkiewicz" <[email-masked]>
Message-Id: <[email-masked]>
Date: Mon, 23 Sep 1996 13:36:11 -0500
In-Reply-To: Zhou Feng <[email-masked]>
        "CCL:(no subject)" (Sep 23, 11:32am)
References: <[email-masked]>
X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail)
To: Zhou Feng <[email-masked]>, [email-masked]
Subject: Re: CCL:(no subject)
Cc: [email-masked]
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Status: RO

On Sep 23, 11:32am, Zhou Feng wrote:
> Subject: CCL:(no subject)
> Hi:
>
>  I am looking for a reasonably accurate implicit solvation energy program
which
> can do some simple energy minimization or low temperature MD to predict the
> energies of a biomoleular system, there are moderate conformational changes
> which has to be predicted along with the energies. IS there anyone who can
give
> me some suggestions?  We have CHARMM & Delphi, but we need to do some
dynamics
> with the implicit solvent model.
>
> Feng Zhou
> Argonne National Lab.

An excellent program FANTOM written by Werner Braun and co-workers can do
that. Please, refer to the following web page for information:

http://www.hbcg.utmb.edu/faculty/braun/fm_home.html

FANTOM is free of charge for academic users.

Regards,

Robert Fraczkiewicz,
University of Texas Medical Branch

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To: Zhou Feng <[email-masked]>
Subject: Solvent model in mole. mech.
Status: RO

   Dear Feng,

     The Incorporation of Hydration Forces Determined by Continuum
     Electrostatics into Molecular Mechanics Simulations,
     R.J. Zauhar, J. Comp. Chem., 12, 575-83 (1991).

  I do not yet have this working with my new code, but it is not difficult
  to make the modifications. Let me know if you are interested in this.

       Best regards,

       Randy

All opinions expressed here are mine, not my employer's

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>From [email-masked] Mon Sep 23 14:01:27 1996
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Date: Mon, 23 Sep 1996 14:00:55 -0500 (CDT)
From: Rino Ragno <[email-masked]>
To: Zhou Feng <[email-masked]>
Subject: Re: CCL:(no subject)
Status: RO

On Mon, 23 Sep 1996, Zhou Feng wrote:

> Hi:
>
>  I am looking for a reasonably accurate implicit solvation energy program
which
> can do some simple energy minimization or low temperature MD to predict the
> energies of a biomoleular system, there are moderate conformational changes
> which has to be predicted along with the energies. IS there anyone who can
give
> me some suggestions?  We have CHARMM & Delphi, but we need to do some
dynamics
> with the implicit solvent model.
>
>
>
> Feng Zhou
> Argonne National Lab.
>
>

Hi,

Have a look to the TINKER program which is free:
http://dasher.wustl.edu/tinker/

It has a GB/SA module!

Rino

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||  Institute for Biomedical Computing            or: [email-masked]     ||
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From: Craig Burkhart <[email-masked]>
Organization: Goodyear Research
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To: Zhou Feng <[email-masked]>
Subject: Re: CCL:(no subject)
References: <[email-masked]>
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>
>  I am looking for a reasonably accurate implicit solvation energy program
which
> can do some simple energy minimization or low temperature MD to predict the
> energies of a biomoleular system, there are moderate conformational changes
> which has to be predicted along with the energies. IS there anyone who can
give
> me some suggestions?  We have CHARMM & Delphi, but we need to do some
dynamics
> with the implicit solvent model.
>

Try contacting Clark Still's group at Columbia. Macromodel may do what you
need...

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From: JOE KLIMKOWSKI <[email-masked]>
Subject: Implicit Solvation
To: [email-masked]
Cc: KLIMKOWSKI V JOE <[email-masked]>
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Status: RO

Feng,

  I saw you message on the Computational chemistry BB. Since you have CHARMM
you should consider the ASP (atomic solvation parameter) method of
Wesson and Eisenberg. It is implemented in both the academic and MSI
versions of CHARMM. Unfortunatly the documentation for it is almost
nonexistent. A grep in the /quanta/data/doc subdirectory will confirm
it's existance, but not much else.

  Another good package you might want to consider is Jay Ponder's
TINKER. It includes Still's GB/SA method. Possibly some others.

Best Regards,

V. Joe Klimkowski

Eli Lilly and Company

From: Thomas Simonson <[email-masked]>
Message-Id: <[email-masked]>
To: [email-masked]
Subject: Re: CCL:(no subject)
Status: RO

Dear Feng,

Xplor has a simple and fast excluded volume implicit solvent model,
although this may not yet be in the official version. But there's
just a small piece of code to add, which you can probably obtain
from Axel Brunger. The original reference for this model is
Colonna & Sander, 1990, Biophys.J. 57:1103, and Chris Sander has
published more recent papers using it. It's similar to an accessible
surface area, but faster.

Tom Simonson

Regards,From: A J Turner <[email-masked]>
To: Zhou Feng <[email-masked]>
Subject: Re: CCL:(no subject)
In-Reply-To: <[email-masked]>
Message-Id: <[email-masked]>
Mime-Version: 1.0
Content-Type: TEXT/PLAIN; charset=US-ASCII
Status: RO

Hi!

Have you check out the new polarisable boundary terms in mff in CHARMM 24?

Cheers

Alex

 -------------------------------------------------------------------
|Alexander J Turner         [email-masked]                  |
|Post Graduate              |http://www.bath.ac.uk/~chpajt/home.html|
|School of Chemistry        |+144 1225 8262826 ext 5137             |
|University of Bath         |                                       |
|Bath, Avon, U.K.           |Field: QM/MM modeling                  |
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From: "Ernest Chamot" <[email-masked]>
Subject: Re: CCL:(no subject)
To: "Zhou Feng" <[email-masked]>
X-Mailer: VersaTerm Link v1.1.6
Status: RO

Hi Feng,

> I am looking for a reasonably accurate implicit solvation energy program
which
>can do some simple energy minimization or low temperature MD to predict the
>energies of a biomoleular system, there are moderate conformational changes
>which has to be predicted along with the energies.

There are a couple very effective implicit solvation models that I know of
and can recommend, but they are both implemented for semiempirical QM
methods, rather than molecular mechanics.  COSMO by Klamt in MOPAC and SM2
(or SM5 now?) by Cramer and Truhlar in Amsol have picked up some pretty
subtle geometric effects that are completely missed by simpler SCRF models
(which assume only a spherical cavity.)  Is your system small enough to
model semiempirically?

EC
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