From chemistry-request@server.ccl.net Fri Jan 18 08:45:06 2002 Received: from kodakr.kodak.com ([192.232.119.69]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0IDj6I15175 for ; Fri, 18 Jan 2002 08:45:06 -0500 Received: from acadia.image.kodak.com (acadia.image.kodak.com [150.220.67.56]) by kodakr.kodak.com (8.11.1/8.11.1) with ESMTP id g0IDiu708016 for ; Fri, 18 Jan 2002 08:44:56 -0500 (EST) Received: from kodak.com (berlioz.rl.kodak.com [150.220.89.22]) by acadia.image.kodak.com (8.10.2+Sun/8.10.2) with ESMTP id g0IDir001062 for ; Fri, 18 Jan 2002 08:44:53 -0500 (EST) Sender: david.giesen@kodak.com Message-ID: <3C4823F8.70742B7A@kodak.com> Date: Fri, 18 Jan 2002 08:32:40 -0500 From: David J Giesen Organization: Eastman-Kodak X-Mailer: Mozilla 4.05C-SGI [en] (X11; I; IRIX64 6.5 IP25) MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: Re: CCL:Program to calculate con vs time References: <3C443339.2E38BA6C@kodak.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Thank you to all that replied to my request for programs to calculate concentration vs time given a set of rate constants and initial concentrations. Numerous people pointed me to the free download of the CKS program distributed by IBM - http://www.almaden.ibm.com/st/msim/ (that's the QCPE program I mentioned in my original note as 'MSIMPC'). CKS is a nice, simple program with a GUI that works quite well. Thanks go to Steve Cabaniss , Geoff Hutchison , and Sergio Emanuel Galembeck . There is a graphical user interface for Kinsim and Fitsim call KinTekSim that is distributed for free by KinTek Corp at http://www.kintek-corp.com/kinteksim.htm Thanks to George Douglas Markham for the tip and assistance in getting the thing running. KinTekSim appears to be very powerful and flexible, but I've found the interface to be just a bit flaky at times. But hey, it is free! Dave Price was kind enough to e-mail me the Gear program, which also does this. Thanks Dave! Alimet Ozen suggested the commercial program ChemKin (http://www.chemkin.com). Finally, I also found the program Gepasi (http://gepasi.dbs.aber.ac.uk/softw/gepasi.html). It is written by biochemists for biochemists (and thus is capable of dealing with much more complex kinetic problems than our comparably simple work). Of all the programs, this has the slickest interface and most options for computing kinetics. It also appears to be quite stable. In the end, we're either going with CKS or Gepasi, depending on whether simplicity or flexibility/slick GUI arguments win the day. Thanks again, all! Dave David J Giesen wrote: > > Is anyone aware of a non-commercial computer program available to > calculate concentration versus time for a series of reactions with known > rates and known initial conditions? > > I am aware of Kintecus in the CCL archives and http://www.kintecus.com > (very nice, but too expensive), Kinsim from > http://www.biochem.wustl.edu/cflab/message.html (works just fine, but I > was hoping for a bit better interface), and MSIMPC from QCPE > http://qcpe.chem.indiana.edu (which I haven't tried as it costs too much > just to get access). > > That's all I was able to find with all my web and ccl archive searching > tricks. Any other suggestions? > > Dave > -- Dr. David J. Giesen Eastman Kodak Company david.giesen@kodak.com 2/83/RL MC 02216 (ph) 1-716-58(8-0480) Rochester, NY 14650 (fax)1-716-588-1839 From chemistry-request@server.ccl.net Fri Jan 18 10:31:44 2002 Received: from mailhost1.rdg.ac.uk ([134.225.16.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0IFViI17484 for ; Fri, 18 Jan 2002 10:31:44 -0500 Received: from indyp.chemistry ([134.225.168.35] helo=reading.ac.uk) by mailhost1.rdg.ac.uk with esmtp (University of Reading Email Service) id {16RazL-0005yq-00} for CHEMISTRY@www.ccl.net; Fri, 18 Jan 2002 15:31:32 +0000 Sender: dave@ccl.net Message-ID: <3C483F79.49F9B356@reading.ac.uk> Date: Fri, 18 Jan 2002 15:30:01 +0000 From: Dave Price Organization: none-what-so-ever X-Mailer: Mozilla 4.76C-SGI [en] (X11; I; IRIX 6.5 IP22) X-Accept-Language: en MIME-Version: 1.0 To: Comp Chem Mailing List Subject: Atom electron densities Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Fellow Computational Chemists, Does anyone know where I can get my hands on a set of spherically averaged electron densities for heavy atoms? Specifically, I need some actinides. Regards, Dave -- ------------------------------------------------------------------------ Dr. David W. Price MA CChem MRSC Tel: +44 (0)118 9875123 extn 7415 Department of Chemistry, Fax: +44 (0)118 9316331 University of Reading, mailto:d.w.price@reading.ac.uk Whiteknights, READING RG6 6AD U.K. ------------------------------------------------------------------------ From chemistry-request@server.ccl.net Fri Jan 18 14:51:32 2002 Received: from mole.chem.iupui.edu ([134.68.136.192]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0IJpWI21831 for ; Fri, 18 Jan 2002 14:51:32 -0500 Received: from mole.chem.iupui.edu (mole.chem.iupui.edu [134.68.136.192]) by mole.chem.iupui.edu (8.9.1/8.9.1) with ESMTP id OAA277899 for ; Fri, 18 Jan 2002 14:50:51 -0500 (EST) Date: Fri, 18 Jan 2002 14:50:51 -0500 From: Daquan Gao To: chemistry@ccl.net Subject: RE: Autodock In-Reply-To: <3C45DF59@ntserver-e2w2.tcd.ie> Message-ID: MIME-Version: 1.0 Content-Type: MULTIPART/MIXED; BOUNDARY="-2042328896-1037458783-1011383451=:277578" This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. Send mail to mime@docserver.cac.washington.edu for more info. ---2042328896-1037458783-1011383451=:277578 Content-Type: TEXT/PLAIN; charset=US-ASCII This is another attempt to answer to the question about autodock. I lost his email, so to everyone, bear with me, ssh. Okay, I just modified the script mkdpf3, it now can work whether the input files are in the current dir or not. Anyway, I saw the problem, and I resolved it. Hope Autodock people may thank me, kidding. Daquan ---2042328896-1037458783-1011383451=:277578 Content-Type: TEXT/PLAIN; charset=US-ASCII; name=testmkdpf3 Content-Transfer-Encoding: BASE64 Content-ID: Content-Description: Content-Disposition: attachment; filename=testmkdpf3 IyEgL2Jpbi9jc2gNCiMNCiMgVXNhZ2U6IG1rZHBmMyBsaWdhbmQucGRicSBt YWNyb21vbC5wZGJxcw0KIyBOZWVkczogZHBmM2dlbiAoQVdLIHByb2dyYW0p DQojDQplY2hvICdcDQpfX19fX19fX19fX19fX19fX19fX19fX19fX19fX19f X19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19f X19fX1wNCm1rZHBmM1wNCihDKSAxOTk5LCBHYXJyZXR0IE1vcnJpcywgVFNS SS5cDQpcDQpMaWdhbmQgPSAiJyQxJyIsIE1hY3JvbW9sZWN1bGUgPSAiJyQy JyIuXA0KXA0KTWFraW5nICInJDE6cicuJyQyOnInLmRwZiIsICBiYXNlZCBv biB0aGUgYXRvbSB0eXBlcyBmb3VuZCBpbiAiJyQxJyJcDQpcDQouLi5Vc2lu ZyAiZHBmM2dlbiIuXA0KJw0Kc2V0IG9uZSA9ICQxOnQNCnNldCB0d28gPSAk Mjp0DQoNCmRwZjNnZW4gJDEgPiEgJG9uZTpyJy4nJHR3bzpyLmRwZg0KDQpz ZWQgJ3MvPG1hY3JvbW9sPi8nJHR3bzpyJy9nJyAkb25lOnInLickdHdvOnIu ZHBmID4hIHRtcDENCnNlZCAncy88c21sbW9sPi8nJG9uZTpyJy9nJyB0bXAx ID4hIHRtcDINCi9iaW4vbXYgdG1wMiAkb25lOnInLickdHdvOnIuZHBmDQov YmluL3JtIHRtcDENCg0KaWYgKC16ICRvbmU6cicuJyR0d286cicuZHBmJykg dGhlbg0KICAgIC9iaW4vcm0gLWYgJG9uZTpyJy4nJHR3bzpyJy5kcGYnDQog ICAgZWNobyAnXA0KU29ycnksIEkgY291bGQgbm90IGNyZWF0ZSAnJG9uZTpy Jy4nJHR3bzpyJy5kcGZcDQpfX19fX19fX19fX19fX19fX19fX19fX19fX19f X19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19f X19fX19fX1wNCicNCmVsc2UgDQogICAgZWNobyAnXA0KQ29tcGxldGVkIHBy ZXBhcmluZyAnJG9uZTpyJy4nJHR3bzpyJy5kcGZcDQpfX19fX19fX19fX19f X19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19f X19fX19fX19fX19fX19fX19fX19fX1wNCicNCmVuZGlmDQo= ---2042328896-1037458783-1011383451=:277578-- From chemistry-request@server.ccl.net Fri Jan 18 11:09:40 2002 Received: from lauca.usach.cl ([158.170.64.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0IG9dI18077 for ; Fri, 18 Jan 2002 11:09:39 -0500 Received: from danilo ([158.170.51.186]) by lauca.usach.cl (8.10.2+Sun/8.10.2) with ESMTP id g0IG7Mw09103; Fri, 18 Jan 2002 13:07:22 -0300 (CLST) From: "Danilo Gonzalez" To: Cc: Subject: Summary: SASA programs Date: Fri, 18 Jan 2002 13:06:24 -0300 Message-ID: <000201c1a03a$15b4c3c0$ba33aa9e@usach.cl> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0003_01C1A020.F0678BC0" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2627 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 This is a multi-part message in MIME format. ------=_NextPart_000_0003_01C1A020.F0678BC0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi all! =20 Thanks to all, for yours comments. My question was: =20 Somebody know a free program (with sources, if is possible) to calculate the Surface Area Solvent Accessibility (SASA)? =20 In summary the program available for that are: MSMS http://www.scripps.edu/sanner GPOL93 VEGA http://users.unimi.it/~ddl NACCESS http://wolf.bms.umist.ac.uk/naccess/ MolMol Sybyl =20 all the answers are follow, and thanks again: =20 cheers! =20 =20 ************************ Hi, I think sybyl will do what you want. huajun =20 =20 *********************** try http://www.scripps.edu/sanner to find the MSMS program. As I remember, it includes the source. =20 GOOD Lucky!!! =20 ********************************** Look for the GEPOL93 code. It is freeware and able to do the things you want, and more. I found it somewhere on the web. =20 ************************************** =20 Our program VEGA (http://users.unimi.it/~ddl) is able to calculate and display SASA and also other molecular surfaces. It reads a lot of file formats and it runs under several operating systems. =20 -- Dr. Giulio Vistoli Ist. di Chimica Farmaceutica e Tossicologica Viale Abruzzi, 42 I-20131 Milano (Italy) Tel. +39-02-58357522 Fax +39-02-58357565 E-Mail: giulio.vistoli@unimi.it WWW: http://users.unimi.it/~ddl =20 =20 ***************************** =20 There is the program MSMS of Michel Sanner that compute solvent excluded surface (SES) and that should also compute Solvent Accessible (SAS). Try also the Vega package.=20 I do not have the link right now but you should find it easily with a good search engine. =20 Cheers, --=20 Fabien Fontaine Engineer in Biotechnology Research Group on Biomedical Informatics, IMIM/UPF Doctor Aiguader, 80 E-08003 Barcelona (SPAIN) Tel: (34) 93 221 1009 Ext: 2340 Fax: (34) 93 221 3237 ********************************* NACCESS http://wolf.bms.umist.ac.uk/naccess/ =20 cheers, =20 Malcolm -- Malcolm Gillies Post-doctoral researcher Organic Chemistry, Dept Chemistry, Technical University of Denmark =20 =20 =20 *********************************** Dear Mr. Gonzalez, =20 there are several programs to calculate the surface of molecules. A good point to start is Michael Sanners MSMS.The Swiss-PDB Viewer can calculate the surface of proteins. gOpenMol can calculate the Connolly surface. Molekel has a version of MS, which also can calculate Connolly surfaces. =20 Hope this helps, =20 ------------------------------------------------- Christoph Nimptsch Apotheker Pharmazeutisches Institut Arbeitskreis Prof. Kovar Universit=E4t T=FCbingen Auf der Morgenstelle 8 D-72076 Tuebingen Tel.: 07071/2978794 mailto:christoph.nimptsch@uni-tuebingen.de ------------------------------------------------- =20 =20 **************** MolMol will do it. It has nice graphical interface and source is provided. =20 Hope this helps, =20 Mire Zloh School of Pharmacy 29 Brunswick Square London WC1N 1AX=20 =20 ************************* try Michel F. SANNER's MSMS: =20 Sanner, M.F., Spehner, J.-C., and Olson, A.J. (1996) Reduced surface: an efficient way to compute molecular surfaces. Biopolymers, Vol. 38., (3), 305-320. =20 you can get @ http://www.scripps.edu/sanner. =20 hope it helps & best regards =20 felipe =20 =20 ************************** =20 I recently used SIMS, by Yury N. Vorobjev (Biophysical Journal,73:722-732; 1997); You can get the free source software at: =20 http://femto.med.unc.edu/SIMS/ =20 Fran=E7ois Sampieri =20 =20 ****************************************** Actually, it is in the CCL archives: =20 http://www.ccl.net/cca/software/SOURCES/FORTRAN/molecular_surface/gepol9 3/index.shtml =20 --=20 Marcel Swart =20 Theoretische Chemie (MSC) / Moleculaire Dynamica (GBB) Rijksuniversiteit Groningen Nijenborgh 4 9747 AG Groningen The Netherlands m.swart@chem.rug.nl http://go.to/m.swart ******************************** =20 that=92s all.. =20 ........................................................................ ................... Danilo Gonzalez-Nilo University of Santiago of Chile Faculty of Chemistry and Biology Casilla 40, Correo 33, Santiago - Chile. =20 ------=_NextPart_000_0003_01C1A020.F0678BC0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Hi all!

 

Thanks to all, for yours = comments.

My question =A0was:=

 

Somebody know a free program (with sources, if is = possible) to calculate the Surface Area Solvent Accessibility = (SASA)?

 

In summary the program available for that = are:

MSMS=A0 = http://www.scripps.edu/sanner<= o:p>

GPOL93

VEGA=A0 http://users.unimi.it/~ddl

NACCESS=A0=A0=A0 http://wolf.bms.umist.ac.uk= /naccess/

MolMol

Sybyl

 

all the answers are follow, and thanks again:

 

cheers!

 

 

************************

Hi, I think sybyl will do what you want. huajun

 

 

***********************

try http://www.scripps.edu/sanner = to find the MSMS program. As I remember, it includes the = source.

 

GOOD Lucky!!!

 

**********************************

Look for the GEPOL93 code. It is freeware and able to do the = things you want,

and more. I found it = somewhere on the web.

 

**************************************

 

Our program VEGA (http://users.unimi.it/~ddl) is able to calculate and display SASA and also other molecular surfaces. = It reads a lot of file formats and it runs under several = operating systems.

 

 --
Dr. Giulio Vistoli
Ist. di Chimica Farmaceutica e Tossicologica
Viale Abruzzi, = 42
I-20131 Milano (Italy)
Tel. +39-02-= 58357522
Fax +39-02-58357565
E-Mail: giulio.vistoli@unimi.it<= /font>
WWW: http://users.unimi.it/~ddl

 

 

*****************************

 

There is the program MSMS of Michel Sanner that = compute solvent excluded surface (SES) and that should also compute Solvent = Accessible (SAS). Try also the Vega package.

I do not have the link right now but you should find it easily with a good = search engine.

 

Cheers,

--

Fabien Fontaine

Engineer in Biotechnology

Research Group on Biomedical Informatics, IMIM/UPF

Doctor Aiguader, 80

E-08003 Barcelona = (SPAIN)

Tel: (34) 93 221 1009 Ext: 2340

Fax: (34) 93 221 3237

*********************************

=A0=A0 = NACCESS

=A0=A0=A0 http://wolf.bms.umist.ac.uk= /naccess/

 

cheers,

 

Malcolm

--

Malcolm Gillies = <malcolm.gillies@kemi.dtu.dk>

Post-doctoral researcher

Organic Chemistry, Dept Chemistry,

Technical University of Denmark

 

 

 

***********************************

Dear Mr. Gonzalez,

 

there are several programs to calculate the surface of molecules. A good point to start is Michael Sanners MSMS.The = Swiss-PDB Viewer can calculate the surface of proteins. gOpenMol can calculate the Connolly surface. Molekel = has a version of MS, which also can calculate Connolly = surfaces.

 

Hope this helps,

 

-------------------------------------------------=

Christoph Nimptsch

Apotheker

Pharmazeutisches Institut

Arbeitskreis Prof. Kovar

Universit=E4t T=FCbingen

Auf der Morgenstelle = 8

D-72076 Tuebingen

Tel.: 07071/2978794

mailto:christoph.nimp= tsch@uni-tuebingen.de

-------------------------------------------------=

 

 

****************

MolMol will do it. It has nice graphical interface and source is = provided.

 

Hope this helps,

 

Mire Zloh

School of Pharmacy

29 Brunswick Square

London WC1N 1AX

 

*************************

try Michel F. SANNER's = MSMS:

 

Sanner, M.F., Spehner, J.-C., and Olson, A.J. (1996) = Reduced surface: an efficient way to compute molecular surfaces. Biopolymers, = Vol. 38., (3), 305-320.

 

you can get @ http://www.scripps.edu/sanner.=

 

hope it helps & best regards

 

felipe

 

 

**************************

 

I recently used SIMS, by Yury N. Vorobjev=A0 (Biophysical = Journal,73:722-732; 1997); You can get the free source software = at:

 

http://femto.med.unc.edu/SIMS/

 

Fran=E7ois Sampieri

 

 

******************************************<= /span>

Actually, it is in the CCL = archives:

 

http://www.ccl.net/cca/software/SOURCES/FORTRAN/molecu= lar_surface/gepol93/index.shtml

 

--

Marcel = Swart

 

Theoretische Chemie (MSC) / = Moleculaire Dynamica (GBB)

Rijksuniversiteit = Groningen

Nijenborgh = 4

9747 AG Groningen

The = Netherlands

m.swart@chem.rug.nl

http://go.to/m.swart<= /font>

********************************

 

that’s = all..

 

................................................= ...........................................

Danilo = Gonzalez-Nilo

University of Santiago of Chile<= span style=3D'mso-no-proof:yes'>

Faculty of Chemistry and = Biology

Casilla 40, Correo = 33,

Santiago - = Chile<= span style=3D'mso-no-proof:yes'>.

 

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