From chemistry-request@ccl.net Sat Sep 13 07:03:08 2003 Received: from IPOfCard1.guest-tek.com ([12.31.15.114]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8DB33BS018790 for ; Sat, 13 Sep 2003 07:03:04 -0400 Received: from cosmologic.de ([10.0.0.215]) by IPOfCard1.guest-tek.com (8.11.6/8.11.6) with ESMTP id h8DB1Xc02205; Sat, 13 Sep 2003 07:01:33 -0400 Message-ID: <3F62F958.4040501(at)cosmologic.de> Date: Sat, 13 Sep 2003 13:02:48 +0200 From: Andreas Klamt User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en-us, en MIME-Version: 1.0 To: "Deng, Jun" CC: "chemistry(at)ccl.net" Subject: Re: CCL:Summary on solvent effect References: <3251EC702A37B9458A01D917C3D3B389034FF3(at)sgofusr20.nac.ppg.com> Content-Type: multipart/alternative; boundary="------------010201010703030203080206" X-Spam-Status: No, hits=3.7 required=7.0 tests=EMAIL_ATTRIBUTION,HTML_00_10,HTML_MESSAGE, RCVD_IN_OSIRUSOFT_COM,REFERENCES,USER_AGENT_MOZILLA_UA, X_ACCEPT_LANG,X_OSIRU_OPEN_RELAY version=2.55 X-Spam-Level: *** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) --------------010201010703030203080206 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Sorry for my late answer. We have some experience with reactions in solution. Our finding (and that of several of our customers from industry) is that the following scheme is most useful: - optimize educts and products with DFT in the gasphase (basis set about TZVP or similar, DFT-functional less relevant) - then calculate single point gasphase energies at the best level you can afford . - for frequencies in gasphase it should be sufficient to do that on DFT level. - repeat optimization with COSMO (either in TURBOMOLE or in G03) and get the dielectric energy reductions. (We consider geometry optiization to be essential at least for ions. In TURBOMOLE the geometry optimization with COSMO is very stable! - Finally you should add a statistical thermodynamics corrections (COSMO-RS) with our COSMOtherm program in order to get realistic solvation free energies in arbitrary solvents and solvent mixtures at variable temperature. Regards Andreas Deng, Jun wrote: >First, I'd like to thank all who replied. The information is very valuable to me. > >The original question: >Dear Colleagues: >I am using G98 to calculate the Gibbs free energy of the reaction in the solvent. The reaction involve ionic species, so the solvent effect is important. Here is what I did: > >1. Gas phase geometry optimization and freq calculation >2. Using PCM to calculate single point energy >3. Add thermal correction energy from gas phase to single point energy calculated in solvent. > >Strictly, I think it is better to do geom. optimization and freq. calc. in solvent. However, I couldn't do this in G98 with PCM. Do you have any experience in how important it is to calculate reaction energy with optimized geometry and freq in solvent? > >Reply from Dr. Zhijian Wu: >Hi, > >I think it is better to optimize the geometry and make freq calculation using solvent model, especially for species with net charge by use of PCM or CPCM model. It is ture that it is hard to optimize the structure using PCM or CPCM, but it can be done by carefully chosen the TSARE. And it seems G03 is more powerful in this aspect. > >Recently, we have calculaed charged species with Onsager model. (Jacs, 125(2003)3642, Jacs, 125(2003)6994) > >Hope it helps. > > >Reply from Alessandro Contini: > >Hi Jun, >see Champagne, B et all., Chem. Phys, 238 (1998) 153-163 for a good reference >on PCM and the importance of optimizing with solvent. >Hope this help > > >Reply from Valentin Ananikov: >Hi! > >The approach you have described will be accurate enough >in most cases even if ionic compounds are involved. >Energy hypersurfaces in solution are very flat, so >reoptimization with PCM may have only a little effect. > >We have used this approach for charged transition metal >complexes and found it very useful. > >J.Am.Chem.Soc., 2002, 124, 2839-2852 >Organometallics, 2001, 20, 1652-1667. > >Reply from Jeremy Greenwood: >Hi Jun Deng, > > > >>I am using G98 to calculate the Gibbs free energy of the reaction in the solvent. The reaction involve ionic species, so the solvent effect is important. Here is what I did: >> >>1. Gas phase geometry optimization and freq calculation >>2. Using PCM to calculate single point energy >>3. Add thermal correction energy from gas phase to single point energy calculated in solvent. >> >> > >That's how I used to do it. Still do if optimisation in solution fails. > > > >>Strictly, I think it is better to do geom. optimization and freq. calc. in solvent. However, I couldn't do this in G98 with PCM. Do you have any experience in how important it is to calculate reaction energy with optimized geometry and freq in solvent? >> >> > >Maybe it depends on your system. I've switched to using IEF-PCM in G03 >-- this method gives analytical 2nd derivatives which makes optimisation >of ionic species in solution much less troublesome, and also makes it >easy to calculate thermal corrections at the solution-phase geometry. >Whether or not any continuum method is going to be realistic enough >is another matter. > > > > > > > >-= This is automatically added to each message by the mailing script =- >To send e-mail to subscribers of CCL put the string CCL: on your Subject: line >and send your message to: CHEMISTRY(at)ccl.net > >Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST(at)ccl.net >HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > >If your mail is bouncing from CCL.NET domain send it to the maintainer: >Jan Labanowski, jkl(at)ccl.net (read about it on CCL Home Page) >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > > > -- -------------------------------------------------------------------------------- Dr. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt(at)cosmologic.de web: www.cosmologic.de -------------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics -------------------------------------------------------------------------------- --------------010201010703030203080206 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Sorry for my late answer.

We have some experience with reactions in solution. Our finding (and that of several of our customers from industry) is that the following scheme is most useful:
- optimize educts and products with DFT in the gasphase (basis set about TZVP or similar, DFT-functional less relevant)
- then calculate single point gasphase energies at the best level you can afford .
- for frequencies in gasphase it should be sufficient to do that on DFT level.
- repeat optimization with COSMO (either in TURBOMOLE or in G03) and get the dielectric energy reductions. (We consider geometry optiization to be essential at least for ions. In TURBOMOLE the geometry optimization with COSMO is very stable!
- Finally you should add a statistical thermodynamics corrections (COSMO-RS) with our COSMOtherm program in order to get realistic solvation free energies in arbitrary solvents and solvent mixtures at variable temperature.

Regards

Andreas


Deng, Jun wrote:
First, I'd like to thank all who replied.  The information is very valuable to me.

The original question:
Dear Colleagues:
I am using G98 to calculate the Gibbs free energy of the reaction in the solvent.  The reaction involve ionic species, so the solvent effect is important.  Here is what I did:

1. Gas phase geometry optimization and freq calculation
2. Using PCM to calculate single point energy
3. Add thermal correction energy from gas phase to single point energy calculated in solvent.

Strictly, I think it is better to do geom. optimization and freq. calc. in solvent.  However, I couldn't do this in G98 with PCM.  Do you have any experience in how important it is to calculate reaction energy with optimized geometry and freq in solvent?

Reply from Dr. Zhijian Wu:
Hi,

I think it is better to optimize the geometry and make freq calculation using solvent model, especially for species with net charge by use of PCM or CPCM model. It is ture that it is hard to optimize the structure using PCM or CPCM, but it can be done by carefully chosen the TSARE. And it seems G03 is more powerful in this aspect.

Recently, we have calculaed charged species with Onsager model. (Jacs, 125(2003)3642, Jacs, 125(2003)6994) 

Hope it helps.

 
Reply from Alessandro Contini:

Hi Jun,
see Champagne, B et all., Chem. Phys, 238 (1998) 153-163  for a good reference 
on PCM and the importance of optimizing with solvent.
Hope this help


Reply from Valentin Ananikov:
Hi!

The approach you have described will be accurate enough
in most cases even if ionic compounds are involved.
Energy hypersurfaces in solution are very flat, so
reoptimization with PCM may have only a little effect.

We have used this approach for charged transition metal
complexes and found it very useful.

J.Am.Chem.Soc., 2002, 124, 2839-2852 
Organometallics, 2001, 20, 1652-1667.

Reply from Jeremy Greenwood:
Hi Jun Deng,

  
I am using G98 to calculate the Gibbs free energy of the reaction in the solvent.  The reaction involve ionic species, so the solvent effect is important.  Here is what I did:

1. Gas phase geometry optimization and freq calculation
2. Using PCM to calculate single point energy
3. Add thermal correction energy from gas phase to single point energy calculated in solvent.
    
 
That's how I used to do it. Still do if optimisation in solution fails.

  
Strictly, I think it is better to do geom. optimization and freq. calc. in solvent.  However, I couldn't do this in G98 with PCM.  Do you have any experience in how important it is to calculate reaction energy with optimized geometry and freq in solvent?
    
 
Maybe it depends on your system. I've switched to using IEF-PCM in G03 
-- this method gives analytical 2nd derivatives which makes optimisation 
of ionic species in solution much less troublesome, and also makes it
easy to calculate thermal corrections at the solution-phase geometry. 
Whether or not any continuum method is going to be realistic enough 
is another matter.


 




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-- 
--------------------------------------------------------------------------------
Dr. Andreas Klamt
COSMOlogic GmbH&CoKG
Burscheider Str. 515
51381 Leverkusen, Germany

Tel.: +49-2171-73168-1  
Fax:  +49-2171-73168-9
e-mail: klamt(at)cosmologic.de
web:    www.cosmologic.de
--------------------------------------------------------------------------------
COSMOlogic
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--------------010201010703030203080206-- From chemistry-request@ccl.net Fri Sep 12 13:39:20 2003 Received: from gip2.u-picardie.fr (gip2.u-picardie.fr [193.49.184.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8CHcnkK023256 for ; Fri, 12 Sep 2003 13:38:49 -0400 Received: by gip2.u-picardie.fr (Postfix, from userid 33) id 4A92F71AB; Fri, 12 Sep 2003 19:38:49 +0200 (CEST) To: chemistry(at)ccl.net Subject: AmberFFC v1.3 released Message-ID: <1063388329.3f6204a939b22(at)webmail.u-picardie.fr> Date: Fri, 12 Sep 2003 19:38:49 +0200 (CEST) From: FyD Cc: fduprado(at)scripps.edu MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: IMP/PHP IMAP webmail program 2.2.6 X-Spam-Status: No, hits=0.0 required=7.0 tests=USER_AGENT version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear All, I am pleased to announce the release of AmberFFC version 1.3. In its original version, AmberFFC was designed to convert six AMBER force fields (parm91, parm91X, parm94, parm96, parm98 & parm99) freely available in the public domain (http://amber.scripps.edu & http://amber.scripps.edu/dbase.html), for use with commercial molecular modeling packages, using the Accelrys (http://www.accelrys.com/) software package as a case model. With the version 1.2, AmberFFC converts three GLYCAM force fields (GLYCAM_93 and two new GLYCAM versions) developed by Woods et al. (http://glycam.ccrc.uga.edu). With the version 1.3, a modification of the parm99 version (Simmerling et al.) and the GAFF force fields are also converted. The AmberFFC web site has slightly changed: http://www.u-picardie.fr/labo/lbpd/AmberFFC/ Regards, Francois F.-Y. Dupradeau -- The Scripps Research Institute, San Diego, CA Faculte de Pharmacie, UPJV, Amiens, France -- http://www.u-picardie.fr/labo/lbpd/fyd.htm From chemistry-request@ccl.net Sat Sep 13 12:12:19 2003 Received: from dirf.bris.ac.uk (dirf.bris.ac.uk [137.222.10.72]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8DGCEBS012609 for ; Sat, 13 Sep 2003 12:12:15 -0400 Received: from eis.bris.ac.uk by dirf.bris.ac.uk with SMTP-PRIV with ESMTP; Sat, 13 Sep 2003 17:10:10 +0100 Received: from simpson (simpson.chm.bris.ac.uk [137.222.42.59]) by eis.bris.ac.uk (8.11.6p2/8.11.6) with SMTP id h8DG8KS27465 for ; Sat, 13 Sep 2003 17:08:20 +0100 (BST) Message-ID: <006d01c37a12$04f486c0$3b2ade89~at~chm.bris.ac.uk> From: Chris Arthur To: CHEMISTRY Subject: CCL: Autodock and Rigid Body Docking Date: Sat, 13 Sep 2003 17:13:50 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2720.3000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-Spam-Status: No, hits=3.5 required=7.0 tests=RCVD_IN_OSIRUSOFT_COM,X_OSIRU_OPEN_RELAY version=2.55 X-Spam-Level: *** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi I would like to try to dock a small protein (88aa) to a larger one (300ish aa) - now I know autodock is really designed for small molecules but i was wondering if there was any way to get it to essentially run a rigid body dock of these two together? and if so, how i would go about it? or if thats not possible to limit the flexibility of the small protein so that only considers side chain rotation/flexibility and not the whole protein Thanks in advance Chris