Amsol compiling

From chemistry-request@server.ccl.net Thu Feb 28 22:03:46 2002 Received: from red.CACheSoftware.com (IDENT:root@[12.17.172.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2133j516072 for ; Thu, 28 Feb 2002 22:03:45 -0500 Received: from daveg.cachesoftware.com ([192.168.110.100]) by red.CACheSoftware.com (8.11.6/8.9.3/3) with ESMTP id g2131qg19511; Thu, 28 Feb 2002 19:01:52 -0800 Message-Id: <5.1.0.14.0.20020222161041.039d25f0@pop3.norton.antivirus> X-Sender: daveg/mail.cachesoftware.com@pop3.norton.antivirus (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Thu, 28 Feb 2002 19:06:17 -0800 To: chemistry@ccl.net From: David Gallagher Subject: AGENDA: MOPAC User Group (MUG) Meeting, Orlando ACS Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_85371256==_.ALT" --=====================_85371256==_.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed MOPAC User Group (MUG) Meeting, Orlando ACS The second Mopac Users Group (MUG) Meeting, scheduled for 1pm - 4pm on Sunday April 7, 2002, at the Sheraton Hotel (Florida Bay 2) in conjunction with the Spring ACS Meeting in Orlando, FL. PRELIMINARY AGENDA: 01.00 Introduction George Vacek, Schrodinger Inc. Portland, OR 01.05 WebMO: A Web-based Interface for MOPAC, William Polik et al, Dept. of Chemistry, Hope College, MI 01.25 Effects of Hydration on the Molecular Structure of Atrazine Dimers. A MOPAC PM3 Study. Robert Carper et al, Dept. of Chem., Wichita State Univ., KS 01.45 MOPAC Calculations of the electrostatic potential inside the potassium channel. Comparison with molecular mechanics. Andrey Bliznyuk, Australian Nat. Univ., Canberra, Australia 02.05 PM5: A New Higher Accuracy Method for MOPAC James Stewart, Stewart Computational Chemistry, Colorado Springs, CO 02.20 MOPAC Q&A Session James Stewart, Stewart Computational Chemistry, Colorado Springs, CO 02.30 BREAK 02.50 A New Method for Locating Active Sites in Enzymes George Vacek, Schrodinger Inc. Portland, OR 03.10 Luminescence of silica ring clusters Jeliazko Polihronov, Univ. Florida. FL 03.30 Computational Chemistry for the Chemistry Educator, and the National Computational Science Institute Robert Gotwals The Shodor Education Foundation, Durham, NC 03.50 Summary of new Capabilities in MOPAC 2002 David Gallagher, Fujitsu, Portland OR 04.00 CLOSE Abstracts can be found at http://www.cachesoftware.com/mug/ and http://www.schrodinger.com/Announce/Workshop/W2002/mug.html The meeting is sponsored by Fujitsu and attendance is free, but as space is limited please register by Web: http://www.cachesoftware.com/mug/ or http://www.schrodinger.com/Announce/Workshop/W2002/mug.html Tel: Kim Hill at (1) 503 746 3602 Email: mailto:khill@cachesoftware.com. David Gallagher --=====================_85371256==_.ALT Content-Type: text/html; charset="us-ascii"         MOPAC User Group (MUG) Meeting, Orlando ACS

The second Mopac Users Group (MUG) Meeting, scheduled for 1pm - 4pm on Sunday April 7, 2002, at the Sheraton Hotel (Florida Bay 2) in conjunction with the Spring ACS Meeting in Orlando, FL.

        PRELIMINARY AGENDA:

01.00   Introduction
        George Vacek, Schrodinger Inc. Portland, OR
01.05   WebMO: A Web-based Interface for MOPAC,
        William Polik et al, Dept. of Chemistry, Hope College, MI
01.25   Effects of Hydration on the Molecular Structure of
        Atrazine Dimers. A MOPAC PM3 Study.
        Robert Carper et al, Dept. of Chem., Wichita State Univ., KS
01.45   MOPAC Calculations of the electrostatic potential inside the
        potassium channel. Comparison with molecular mechanics.
        Andrey Bliznyuk, Australian Nat. Univ., Canberra, Australia
02.05   PM5: A New Higher Accuracy Method for MOPAC
        James Stewart, Stewart Computational Chemistry,
        Colorado Springs, CO
02.20   MOPAC Q&A Session
        James Stewart, Stewart Computational Chemistry,
        Colorado Springs, CO
02.30   BREAK
02.50   A New Method for Locating Active Sites in Enzymes
        George Vacek, Schrodinger Inc. Portland, OR
03.10   Luminescence of silica ring clusters
        Jeliazko Polihronov, Univ. Florida. FL
03.30   Computational Chemistry for the Chemistry Educator,
        and the National Computational Science Institute
        Robert Gotwals The Shodor Education Foundation, Durham, NC
03.50   Summary of new Capabilities in MOPAC 2002
        David Gallagher, Fujitsu, Portland OR
04.00   CLOSE

Abstracts can be found at http://www.cachesoftware.com/mug/ and http://www.schrodinger.com/Announce/Workshop/W2002/mug.html
The meeting is sponsored by Fujitsu and attendance is free, but as space is limited please register by

Web: http://www.cachesoftware.com/mug/
or http://www.schrodinger.com/Announce/Workshop/W2002/mug.html
Tel: Kim Hill at (1) 503 746 3602
Email: mailto:khill@cachesoftware.com.

David Gallagher <dgallagher@cachesoftware.com>

--=====================_85371256==_.ALT-- From chemistry-request@server.ccl.net Thu Feb 28 19:32:06 2002 Received: from relay-2v.club-internet.fr ([194.158.96.113]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g210W5511707 for ; Thu, 28 Feb 2002 19:32:05 -0500 Received: from sungam (vlp4a-53.n.club-internet.fr [212.195.6.53]) by relay-2v.club-internet.fr (Postfix) with SMTP id 3F7371687 for ; Fri, 1 Mar 2002 01:31:36 +0100 (CET) Message-ID: <008d01c1c0b9$8511bee0$3506c3d4@sungam> From: "Julien MICHEL" To: Subject: Linear scaling algorithms for QM calculations Date: Fri, 1 Mar 2002 01:36:33 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: 8bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2919.6600 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6600 Dear CCLers, I recently read a few words about algorithms for pure quantum mechanical calculations that scales linearly with the number of electrons in the system studied. I was surprised to read this as I thought such rate was not feasible for any kind of quantum calculation. I would be curious to read more about these algorithms and how they work. Furthermore, I’d like to know if these algorithms have been used to study fairly big molecular systems such as proteins. I would be glad if someone could point some references or even better internet resources focusing on that topic Julien MICHEL From chemistry-request@server.ccl.net Fri Mar 1 03:46:34 2002 Received: from gattinara.ethz.ch ([129.132.117.159]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g218kX524086 for ; Fri, 1 Mar 2002 03:46:33 -0500 Received: (from mjakusch@localhost) by gattinara.ethz.ch (980427.SGI.8.8.8/980728.SGI.AUTOCF) id JAA08151; Fri, 1 Mar 2002 09:45:57 +0100 (CET) Date: Fri, 1 Mar 2002 09:45:57 +0100 From: Michael Jakusch To: Logean Antoine Cc: chemistry@ccl.net Subject: Re: CCL:A little geometrical problem Message-ID: <20020301094557.A499849@gattinara> References: <000e01c1c077$1751e9d0$2d554f82@hit4> Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mutt 1.0us In-Reply-To: <000e01c1c077$1751e9d0$2d554f82@hit4>; from alogean@aspirine.u-strasbg.fr on Thu, Feb 28, 2002 at 05:43:41PM +0100 On Thu, Feb 28, 2002 at 05:43:41PM +0100, Logean Antoine wrote: > A little geometrical problem : > > Taken a residue in a PDB file, how can I calculate the Cartesian > coordinates of CB when I know the coordinates of N, CA and C, the angle > N-CA-CB, C-CA-CB and the bond length CA-CB ? > I think the most general approach is as follows: vn ... vector from CA to N vc ... " C vx ... CB an ... angle N-CA-CB ac ... C-CA-CB ln ... length of vn . . . . . . The scalar product vn . vx = ln * lx * cos an (1). all terms on the right side are known (we know the length of the bond CA-CB!), so (1) is essentially the equation of a plane (the one in which the circle defined by the cone (from the angle) and the sphere (of radius lx around CA) lies). Intersecting this plane with the other one (vc, etc.) yields a line, the intersections of which with the sphere of radius lx around CA give the position(s) of CB. (Of course there are the three possible cases of 0, 1, or 2 solutions - corresponding to the line not touching, just touching and intersecting the sphere). Regards, Michael -- Dr. Michael Jakusch ETH - Swiss Federal Institute of Technology Department of Applied Biosciences Winterthurerstrasse 190 CH-8057 Zürich Switzerland Phone: +41.1.635 60 71 Fax: +41.1.635 68 84 email: michael.jakusch@pharma.anbi.ethz.ch From chemistry-request@server.ccl.net Fri Mar 1 08:32:31 2002 Received: from fecit-gate.fecit.co.uk ([193.119.134.250]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g21DWV517091 for ; Fri, 1 Mar 2002 08:32:31 -0500 Received: by fecit-gate.fecit.co.uk; id NAA25760; Fri, 1 Mar 2002 13:45:47 GMT Received: from suisei(192.168.101.50) by fecit-gate.fecit.co.uk via smap (V5.0) id xma025748; Fri, 1 Mar 02 13:45:33 GMT Received: from calvin.fecit.co.uk (calvin.fecit.co.uk [192.168.101.124]) by suisei.fecit.co.uk (8.6.9/8.6.9) with ESMTP id NAA04819; Fri, 1 Mar 2002 13:00:42 GMT Date: Fri, 1 Mar 2002 13:32:16 +0000 (GMT) From: Andrew Horsfield X-X-Sender: hfield@calvin.fecit.co.uk To: Julien MICHEL cc: Computational Chemistry List Subject: Re: CCL:Linear scaling algorithms for QM calculations In-Reply-To: <008d01c1c0b9$8511bee0$3506c3d4@sungam> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > I would be curious to read more about these algorithms and how they > work. Furthermore, I'd like to know if these algorithms have been used > to study fairly big molecular systems such as proteins. I would be glad > if someone could point some references or even better internet resources > focusing on that topic A good overview of the theory can be found in the review article Stefan Goedecker, Reviews of Modern Physics 71, 1085 (1999) For data on performance for quantum chemistry applications, the papers of Gustavo Scuseria are useful. For example: J. M. Millam and G. E. Scuseria, Journal of Chemical Physics 106, 5569 (1997) A. Daniels and G. Scuseria, Journal of Chemical Physics 110, 1321 (1999) K. Nemeth and G. Scuseria, Journal of Chemical Physics 113, 6035 (2000) Cheers, Andrew From chemistry-request@server.ccl.net Fri Mar 1 09:01:50 2002 Received: from rbadb1.RBACPXCLU.BAS.ROCHE.COM ([196.3.50.190]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g21E1n517579 for ; Fri, 1 Mar 2002 09:01:49 -0500 Received: from CONVERSION-DAEMON.Roche.COM by Roche.COM (PMDF V6.0-025 #47170) id <01KEUMJAC5HS9BPBT4@Roche.COM> for chemistry@ccl.net; Fri, 01 Mar 2002 14:59:50 +0100 Received: from rbamsemcn1.bas.roche.com (rbamsemcn1.bas.roche.com [145.245.211.139]) by Roche.COM (PMDF V6.0-025 #47170) with ESMTP id <01KEUMJ8DYCE9D2EST@Roche.COM> for chemistry@ccl.net; Fri, 01 Mar 2002 14:59:35 +0100 Received: by rbamsemcn1.bas.roche.com with Internet Mail Service (5.5.2653.19) id ; Fri, 01 Mar 2002 15:00:45 +0100 Content-return: allowed Date: Fri, 01 Mar 2002 15:00:36 +0100 From: "Borosy, Andras {Basi~Basel}" Subject: Unity vs Catalyst To: chemistry@ccl.net Message-id: <5FBD82D1CB46D511AAEA0002A55C6F5203F1679A@rbamsem3.bas.roche.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g21E1o517580 Dear Colleauges, Does anyone has some experience or reference about comparison of Unity and Catalyst? Many thank, András Borosy From chemistry-request@server.ccl.net Fri Mar 1 09:18:44 2002 Received: from ucidoor.unitedcatalysts.com ([208.23.162.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g21EIi518077 for ; Fri, 1 Mar 2002 09:18:44 -0500 Received: by ucidoor.unitedcatalysts.com; (8.8.8/1.3/10May95) id JAA07136; Fri, 1 Mar 2002 09:18:02 -0500 (EST) Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Fri, 01 Mar 2002 09:16:23 -0500 (Eastern Standard Time) Received: from lvlxch01.unitedcatalysts.com ([10.16.100.88]) by lvlmail.unitedcatalysts.com (PMDF V6.0-24 #41777) with ESMTP id <0GSA00CJ3SSQ9E@lvlmail.unitedcatalysts.com>; Fri, 01 Mar 2002 09:12:26 -0500 (EST) Received: by lvlxch01.unitedcatalysts.com with Internet Mail Service (5.5.2650.21) id ; Fri, 01 Mar 2002 09:16:16 -0500 Content-return: allowed Date: Fri, 01 Mar 2002 09:16:15 -0500 From: "Shobe, Dave" Subject: RE: A little geometrical problem To: "'Daquan Gao'" , Ingo Brunberg Cc: alogean@aspirine.u-strasbg.fr, chemistry@ccl.net Message-id: <157A51F55AAAD3119CD70008C7B1629D01C15A05@lvlxch01.unitedcatalysts.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-type: text/plain; charset=iso-8859-1 You're absolutely right--I gave a (partial) solution to the wrong problem. (Having misread angle N-CA-CB for [torsion] angle N-C-CA-CB). --David Shobe -----Original Message----- From: Daquan Gao [mailto:dgao@chem.iupui.edu] Sent: Thursday, February 28, 2002 8:47 PM To: Ingo Brunberg Cc: alogean@aspirine.u-strasbg.fr; chemistry@ccl.net Subject: CCL:A little geometrical problem I thought about this again, found my previous answer was not complete. Condition 2) can be satified when N-CA-C <= 180. If N-CA-C = 180, there are infinitely many solutions; when N-CA-C<180 and equals the sum of the other two angles, one solution. Regards, daquan On Fri, 1 Mar 2002, Ingo Brunberg wrote: > Obviously this problem is not as trivial as it seems. Though I can > think of a rather complicated solution, I just want to point out, that > there is most likely no single solution. The point you are searching > is located on the intersection of two cones with the angles N-CA-CB > and C-CA-CB originating from CA. So there are three different cases: > > 1) N-CA-CB + C-CA-CB < N-CA-C: no solution > 2) N-CA-CB + C-CA-CB = N-CA-C: one solution > 3) N-CA-CB + C-CA-CB > N-CA-C: two solutions > > Seems like the problem leads to a quadratic equation. > > Regards, > > Ingo > > > A little geometrical problem : > > > > Taken a residue in a PDB file, how can I calculate the Cartesian > > coordinates of CB when I know the coordinates of N, CA and C, the angle > > N-CA-CB, C-CA-CB and the bond length CA-CB ? > > > > It seems to be trivial but I am unable to find a solution ! > > > > I am sure that somebody can help me. > > > > In advance thank you > > > > LOGEAN Antoine > > > > > > -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Fri Mar 1 09:42:32 2002 Received: from linux16.theochem.uni-stuttgart.de ([129.69.55.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g21EgW518569 for ; Fri, 1 Mar 2002 09:42:32 -0500 Received: from localhost (teomgs@localhost) by linux16.theochem.uni-stuttgart.de (8.11.3/8.11.2/SuSE Linux 8.11.1-0.5) with ESMTP id g21Eg3L30819; Fri, 1 Mar 2002 15:42:03 +0100 X-Authentication-Warning: linux16.theochem.uni-stuttgart.de: teomgs owned process doing -bs Date: Fri, 1 Mar 2002 15:42:03 +0100 (MET) From: "Dr. Martin Schuetz" To: Julien MICHEL cc: Subject: Re: CCL:Linear scaling algorithms for QM calculations In-Reply-To: <008d01c1c0b9$8511bee0$3506c3d4@sungam> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=X-UNKNOWN Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id g21EgW518570 For coupled cluster methods with linear scaling check references on my web site ---------------------------------------------------------------------------- PD Dr. Martin Schuetz Phone: 0049 (0)711-685-4397 University of Stuttgart Fax: 0049 (0)711-685-4442 Institute for Theoretical Chemistry Pfaffenwaldring 55 Room Nr: 8.161 D-70569 Stuttgart Email: schuetz@theochem.uni-stuttgart.de WWW : http://www.theochem.uni-stuttgart.de/~schuetz/ ---------------------------------------------------------------------------- On Fri, 1 Mar 2002, Julien MICHEL wrote: > Dear CCLers, > > I recently read a few words about algorithms for pure quantum mechanical > calculations that scales linearly with the number of electrons in the system > studied. > I was surprised to read this as I thought such rate was not feasible for any > kind > of quantum calculation. I would be curious to read more about these > algorithms and how they work. Furthermore, I’d like to know if these > algorithms have been used to study fairly big molecular systems such as > proteins. I would be glad if someone could point some references or even > better internet resources focusing on that topic > > Julien MICHEL > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > From chemistry-request@server.ccl.net Fri Mar 1 11:22:07 2002 Received: from ramana.chem.yale.edu ([130.132.25.77]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g21GM7520756 for ; Fri, 1 Mar 2002 11:22:07 -0500 Received: from localhost (ivan@localhost) by ramana.chem.yale.edu (8.9.1/8.9.1) with SMTP id LAA01630 for ; Fri, 1 Mar 2002 11:21:36 -0500 (EST) Date: Fri, 1 Mar 2002 11:21:36 -0500 (EST) From: Ivan Tubert Reply-To: Ivan Tubert To: chemistry@ccl.net Subject: Re: CCL:A little geometrical problem In-Reply-To: <200203010206.DAA15091@oc30.uni-paderborn.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Of course there are up to two solutions! It is possible to reach that conclusion without resorting to cones or equations. Think about the stereochemistry for a moment: The three atoms that you know define a _plane_. The fourth atom can be off the plane on either face, forming either _enantiomer_. If you know the configuration of your aminoacid--usually (L)-- you can choose the correct solution. There is also the degenerate case in which the four atoms are on the same plane, so you have only one solution; and you can have zero solutions if the angles are not wide enough. Ivan Tubert On Fri, 1 Mar 2002, Ingo Brunberg wrote: Obviously this problem is not as trivial as it seems. Though I can think of a rather complicated solution, I just want to point out, that there is most likely no single solution. The point you are searching is located on the intersection of two cones with the angles N-CA-CB and C-CA-CB originating from CA. So there are three different cases: 1) N-CA-CB + C-CA-CB < N-CA-C: no solution 2) N-CA-CB + C-CA-CB = N-CA-C: one solution 3) N-CA-CB + C-CA-CB > N-CA-C: two solutions Seems like the problem leads to a quadratic equation. Regards, Ingo > A little geometrical problem : > > Taken a residue in a PDB file, how can I calculate the Cartesian > coordinates of CB when I know the coordinates of N, CA and C, the angle > N-CA-CB, C-CA-CB and the bond length CA-CB ? > > It seems to be trivial but I am unable to find a solution ! > > I am sure that somebody can help me. > > In advance thank you > > LOGEAN Antoine -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Fri Mar 1 11:12:21 2002 Received: from t12mail.lanl.gov ([128.165.22.99]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g21GCK520634 for ; Fri, 1 Mar 2002 11:12:21 -0500 Received: from there (t12lap6.lanl.gov [128.165.22.56]) by t12mail.lanl.gov (8.9.1a/8.9.1) with SMTP id JAA01074; Fri, 1 Mar 2002 09:11:52 -0700 (MST) Message-Id: <200203011611.JAA01074@t12mail.lanl.gov> Content-Type: text/plain; charset="iso-8859-15" From: Matt Challacombe Reply-To: MChalla@LANL.Gov Organization: Group T-12, Los Alamos National Lab To: "Julien MICHEL" , Subject: Re: CCL:Linear scaling algorithms for QM calculations Date: Fri, 1 Mar 2002 01:58:02 -0700 X-Mailer: KMail [version 1.3.1] References: <008d01c1c0b9$8511bee0$3506c3d4@sungam> In-Reply-To: <008d01c1c0b9$8511bee0$3506c3d4@sungam> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g21GCL520635 Hi Julien, You can have a look at our web site (www.t12.lanl.gov/~mchalla), which is woefully out of date (will bring it to the present soon). It does however have some background papers that you may find relevant. We have a fully O(N) code that is getting close to beta quality, which does the following in TRUE O(N) for 3-D insulating systems: Orthogonalization, solution of SCF equations, exact exchange, exchange-correlation and Coulomb sums. It does geometry optimization and PBCs for pure DFT. -Matt On Thursday 28 February 2002 05:36 pm, Julien MICHEL wrote: > Dear CCLers, > > I recently read a few words about algorithms for pure quantum mechanical > calculations that scales linearly with the number of electrons in the > system studied. > I was surprised to read this as I thought such rate was not feasible for > any kind > of quantum calculation. I would be curious to read more about these > algorithms and how they work. Furthermore, I?d like to know if these > algorithms have been used to study fairly big molecular systems such as > proteins. I would be glad if someone could point some references or even > better internet resources focusing on that topic > > Julien MICHEL > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net > 70 Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: > jkl@ccl.net -- Matt Challacombe, Ph.D. http://www.t12.lanl.gov/~mchalla/ Los Alamos National Laboratory email: MChalla@LANL.Gov Group T-12, Mail Stop B268 phone: (505) 665-5905 Los Alamos, New Mexico 87545 fax: (505) 665-3909 From chemistry-request@server.ccl.net Fri Mar 1 09:56:28 2002 Received: from rwcrmhc53.attbi.com ([204.127.198.39]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g21EuS518975 for ; Fri, 1 Mar 2002 09:56:28 -0500 Received: from daveg.cachesoftware.com ([12.224.212.200]) by rwcrmhc53.attbi.com (InterMail vM.4.01.03.27 201-229-121-127-20010626) with ESMTP id <20020301145551.XHRR2951.rwcrmhc53.attbi.com@daveg.cachesoftware.com>; Fri, 1 Mar 2002 14:55:51 +0000 Message-Id: <5.1.0.14.0.20020301062721.02c5cb90@pop3.norton.antivirus> X-Sender: (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Fri, 01 Mar 2002 07:00:09 -0800 To: "Julien MICHEL" From: David Gallagher Subject: Re: CCL:Linear scaling algorithms for QM calculations Cc: In-Reply-To: <008d01c1c0b9$8511bee0$3506c3d4@sungam> Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_128207419==_.ALT" --=====================_128207419==_.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed One recent publication suggests that the frontier orbitals on the hydrated enzyme (calculated by MOPAC 2000) correlate to the active sites. See: Effects of Hydration on the Electronic Structure of an Enzyme: Implication for Catalytic Function, Kazuki Ohno et al, J. Am. Chem. Soc. 2001, 123, 8161-8162 A MOPAC 2002 SCF on Crambin (641 atom protein) takes less than 3 minutes on a 1,000 MHz Windows PC and uses only 60 MB of memory. MOPAC 2002 with the MOZYME linear scaling algorithm handles up to 20,000 atoms, for full geometry optimizations and reaction coordinates, and includes the COSMO solvent field. The algorithm also scales approximately linearly in memory usage. MOPAC 2002 is available stand-alone or as part of CAChe software suite. As the method is fairly new, there are not many publications on it's application to proteins around just yet. However, there is more information at www.cachesoftware.com David Gallagher, Fujitsu At 01:36 AM 3/1/2002 +0100, Julien MICHEL wrote: >Dear CCLers, > >I recently read a few words about algorithms for pure quantum mechanical >calculations that scales linearly with the number of electrons in the system >studied. >I was surprised to read this as I thought such rate was not feasible for any >kind >of quantum calculation. I would be curious to read more about these >algorithms and how they work. Furthermore, I'd like to know if these >algorithms have been used to study fairly big molecular systems such as >proteins. I would be glad if someone could point some references or even >better internet resources focusing on that topic > >Julien MICHEL --=====================_128207419==_.ALT Content-Type: text/html; charset="us-ascii" One recent publication suggests that the frontier orbitals on the hydrated enzyme (calculated by MOPAC 2000) correlate to the active sites. See:

Effects of Hydration on the Electronic Structure of an Enzyme: Implication for Catalytic Function, Kazuki Ohno et al, J. Am. Chem. Soc. 2001, 123, 8161-8162

A MOPAC 2002 SCF on Crambin (641 atom protein) takes less than 3 minutes on a 1,000 MHz Windows PC and uses only 60 MB of memory.

MOPAC 2002 with the MOZYME linear scaling algorithm handles up to 20,000 atoms, for full geometry optimizations and reaction coordinates, and includes the COSMO solvent field. The algorithm also scales approximately linearly in memory usage. MOPAC 2002 is available stand-alone or as part of CAChe software suite. As the method is fairly new, there are not many publications on it's application to proteins around just yet. However, there is more information at www.cachesoftware.com

David Gallagher, Fujitsu

At 01:36 AM 3/1/2002 +0100, Julien MICHEL wrote:

Dear CCLers,

I recently read a few words about algorithms for pure quantum mechanical
calculations that scales linearly with the number of electrons in the system
studied.
I was surprised to read this as I thought such rate was not feasible for any
kind
of quantum calculation. I would be curious to read more about these
algorithms and how they work. Furthermore, I’d like to know if these
algorithms have been used to study fairly big molecular systems such as
proteins. I would be glad if someone could point some references or even
better internet resources focusing on that topic

Julien MICHEL

--=====================_128207419==_.ALT-- From chemistry-request@server.ccl.net Fri Mar 1 12:50:45 2002 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g21Hoj522114 for ; Fri, 1 Mar 2002 12:50:45 -0500 Received: from postoffice.mail.cornell.edu (postoffice.mail.cornell.edu [132.236.56.7]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id MAA23779 for ; Fri, 1 Mar 2002 12:50:44 -0500 (EST) Received: from cornell.edu ([128.84.182.122]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id MAA25545; Fri, 1 Mar 2002 12:50:03 -0500 (EST) Sender: richard@cornell.edu Message-ID: <3C7FBF4C.FCD1EB75@cornell.edu> Date: Fri, 01 Mar 2002 12:50:04 -0500 From: Richard Gillilan X-Mailer: Mozilla 4.77 [en] (X11; U; Linux 2.4.16 i686) X-Accept-Language: en MIME-Version: 1.0 To: Joe Leonard CC: chemistry@ccl.net Subject: Re: CCL:MMFF94/docking and initial guesses References: <5.1.0.14.1.20020228181403.00a36270@pop.theworld.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Joe: I am currently writing up an article to submit to J. Comp. Chem. on the OrderFour protein-protein docking system I have written based on MMFF94. I'm hoping to have a draft in a couple weeks. I'll also (probably) be including some small-molecule flexible docking results just for validation. I haven't done enough small molecule docking to have a good feel yet for how well it works compared to other forcefields, but I've had some pretty good success in predicting protein-protein interaction sites that helped guide a couple experimental groups in determining what residues to mutate ... but that doesn't really test the internal coordinate part of the forcefield. I would be interested to hear of other's general impression of MMFF94 and it's successor. Richard Gillilan MacCHESS, Cornell (previously CTC) Joe Leonard wrote: > > Folks, > > Searching the CCL archives revealed that the only group which did > docking studies with MMFF94 was CTC back in 97-98. Granted, > this was a quick search, so I might have missed something - have > there been other efforts which show whether this is a good (or bad) > FF for such calculations (flexible ligand, etc)? > From chemistry-request@server.ccl.net Fri Mar 1 13:38:02 2002 Received: from mtiwmhc21.worldnet.att.net ([204.127.131.46]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g21Ic2522748 for ; Fri, 1 Mar 2002 13:38:02 -0500 Received: from dopetec ([138.23.156.82]) by mtiwmhc21.worldnet.att.net (InterMail vM.4.01.03.27 201-229-121-127-20010626) with ESMTP id <20020301183729.EVTA21598.mtiwmhc21.worldnet.att.net@dopetec> for ; Fri, 1 Mar 2002 18:37:29 +0000 Message-ID: <000a01c1c151$25acd500$529c178a@dopetec> From: "Donald Keidel" To: Subject: gaussian: electron density Date: Fri, 1 Mar 2002 10:44:39 -0800 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0007_01C1C10E.168EE150" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 This is a multi-part message in MIME format. ------=_NextPart_000_0007_01C1C10E.168EE150 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello all, I want to use Gaussian to calculate or determine the electron density on = the oxygen atoms of benzoic acids. I want to do this for various = benzoic acids that are different from eachother only in their = substitution at the ortho meta and para positions. I think that benzoic = acids with different elecron densities at the oxygen of the carboxylate = of the benzoate will coordinate to zinc differently with different = affinities. I might be wrong. What method in Gaussian 98 is best = suited for this. I was told to use CHELPG, but I believe that is used = for electrostatic potentials and not electron densities. Thank you to = all. Have a good day. Don --------------------------------------------------- Donald J. Keidel University of California, Riverside Department of Biochemistry and Molecular Biology Riverside, CA 92521 phone: (909) 787-5493 fax: (909) 787-4434 dkeidel397@att.net webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm ------=_NextPart_000_0007_01C1C10E.168EE150 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Hello all,

I want to use Gaussian to calculate or = determine=20 the electron density on the oxygen atoms of benzoic acids. I want = to do=20 this for various benzoic acids that are different from eachother only in = their=20 substitution at the ortho meta and para positions. I think that = benzoic=20 acids with different elecron densities at the oxygen of the carboxylate = of the=20 benzoate will coordinate to zinc differently with different = affinities. I=20 might be wrong. What method in Gaussian 98 is best suited for = this. =20 I was told to use CHELPG, but I believe that is used for electrostatic=20 potentials and not electron densities. Thank you to all. = Have a good=20 day.

Don

---------------------------------------------------
Donald = J.=20 Keidel
University of California, Riverside
Department of = Biochemistry and=20 Molecular Biology
Riverside, CA 92521
phone: (909)=20 787-5493
fax: (909) 787-4434
dkeidel397@att.net
webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm<= BR>

------=_NextPart_000_0007_01C1C10E.168EE150-- From chemistry-request@server.ccl.net Fri Mar 1 14:57:51 2002 Received: from so.sd.lionbioscience.com ([209.68.255.43]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g21Jvp523821 for ; Fri, 1 Mar 2002 14:57:51 -0500 Received: from tempest.sd.lionbioscience.com (tempest.sd.lionbioscience.com [10.8.0.8]) by so.sd.lionbioscience.com (8.11.3/8.11.3) with ESMTP id g21Jv2x13903 for ; Fri, 1 Mar 2002 11:57:02 -0800 (PST) Received: by tempest.sd.lionbioscience.com with Internet Mail Service (5.5.2653.19) id ; Fri, 1 Mar 2002 11:56:37 -0800 Message-ID: From: Stephen Bowlus To: "'chemistry@ccl.net'" Subject: Amsol compiling Date: Fri, 1 Mar 2002 11:56:35 -0800 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C1C15B.3177E410" This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_001_01C1C15B.3177E410 Content-Type: text/plain; charset="iso-8859-1" I am compiling Amsol (QCPE 706) on an Origin 2000, IRIX 6.5. An executable is formed using the .i64 script, with some complaints from compiler and linker which are not noted in the documentation. When run, the program hangs, without the process accumulating any runtime. I have compiled Amsol on R4K systems (and I think R10K) under earlier versions of IRIX without any problems. Does someone have shareable experience with the O2000/Irix6.5 combination? Thanks in advance for any suggestions, Steve Stephen.Bowlus@lionbioscience.com ------_=_NextPart_001_01C1C15B.3177E410 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Amsol compiling

I am compiling Amsol (QCPE 706) on an Origin 2000, = IRIX 6.5. An executable is formed using the .i64 script, with = some complaints from compiler and linker which are not noted in the = documentation. When run, the program hangs, without the process = accumulating any runtime.

I have compiled Amsol on R4K systems (and I think = R10K) under earlier versions of IRIX without any problems. Does = someone have shareable experience with the O2000/Irix6.5 = combination?

Thanks in advance for any suggestions,
Steve

Stephen.Bowlus@lionbioscience.com

------_=_NextPart_001_01C1C15B.3177E410-- From chemistry-request@server.ccl.net Fri Mar 1 14:51:38 2002 Received: from access.etsu.edu ([151.141.99.22]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g21Jpc523739 for ; Fri, 1 Mar 2002 14:51:38 -0500 Received: from dmc ([151.141.29.51]) by ACCESS.ETSU.EDU (PMDF V6.1 #39282) with SMTP id <01KEUM8I3Q6O9LWCZ1@ACCESS.ETSU.EDU> for chemistry@ccl.net; Fri, 01 Mar 2002 14:50:58 -0500 (EST) Date: Fri, 01 Mar 2002 14:51:33 -0500 From: David Close Subject: G98 Dual Processor ?? X-Sender: closed@access.etsu.edu To: chemistry@ccl.net Message-id: <3.0.6.32.20020301145133.009dfcd0@access.etsu.edu> MIME-version: 1.0 X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT To CCL: Several weeks ago I asked for help installing G98 LINUX version on a Dell 530 Dual Processor workstation. Several CCLers sent me helpful suggestions on how to get G98 LINUX working on this machine. This is working now. Many thanks for the help. Now I have a question about the dual processors. What is the best way to utilize this extra power? Run two jobs, each one on a separate processor, or look into parallel G98 code? As I am rather inexperienced in UNIX, I am not at all certain even how to run two jobs at the same time. Any suggestions would be greatly appreciated. One more thing. I often run big jobs strung together with the --link1-- command. This is fine, but jobs tend to finish in the middle of the night. Does anyone know how to start a new job automatically when a big job is finished? I tried to add more --link1--'s to a .com file that was currently executing, and the whole job crashed in just a few minutes. Regards, Dave Close. From chemistry-request@server.ccl.net Fri Mar 1 15:20:18 2002 Received: from mail.rochester.edu (root@[128.151.224.31]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g21KKI524209 for ; Fri, 1 Mar 2002 15:20:18 -0500 Received: from there (ice.chem.rochester.edu [128.151.195.5]) by mail.rochester.edu (8.12.1/8.12.1) with SMTP id g21KJne914284275 for ; Fri, 1 Mar 2002 15:19:49 -0500 (EST) Message-Id: <200203012019.g21KJne914284275@mail.rochester.edu> Content-Type: text/plain; charset="us-ascii" From: weizhuang Reply-To: weiz@mail.rochester.edu To: CHEMISTRY@ccl.net Subject: add solvent molecules explictly to the system in TINKER Date: Fri, 1 Mar 2002 15:30:44 -0500 X-Mailer: KMail [version 1.3.1] MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Hi,guys: I am studying a organic molecule with TINKER, and I want to add chloroform molecules around it as solvent. ( ie. put this molecule in the cell and fill in the rest space of this cell with chloroform molecules ). could anybody give me some suggestion? regards wei From chemistry-request@server.ccl.net Fri Mar 1 16:08:29 2002 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g21L8T525198 for ; Fri, 1 Mar 2002 16:08:29 -0500 Received: from arlen.ccl.net (arlen.ccl.net [192.148.249.10]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id QAA04575 for ; Fri, 1 Mar 2002 16:08:28 -0500 (EST) Date: Fri, 1 Mar 2002 16:08:26 -0500 (EST) From: Jan Labanowski To: chemistry@ccl.net Subject: New Version of PrestoPlot (fwd) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Forwarding to the list: Nice piece of software to do plots. Check also Qmol: http://lancelot.bio.cornell.edu/jason/qmol.html http://zoyd.bio.cornell.edu/jason/ Jan K. Labanowski | phone: 614-292-9279, FAX: 614-292-7168 Ohio Supercomputer Center | Internet: jkl@ccl.net 1224 Kinnear Rd, | http://www.ccl.net/chemistry.html Columbus, OH 43212-1163 | http://www.ccl.net/ ---------- Forwarded message ---------- Date: Fri, 01 Mar 2002 15:56:15 -0500 From: J. D. Gans To: jkl@ccl.net Subject: New Version of PrestoPlot Hello, I have released a new version (1.16) of PrestoPlot, a freely available, windows based 2D plotting tool. Among the many improvements and bug fixes are: (1) Vector plots. (2) Plot arbitrary 1D functions (including cartesian, polar and parametric plots). (3) Perform interactive non-linear curve fitting of 1D data sets with an arbitrary number of fit parameters. (4) Move and resize graphs using the mouse. (5) Zoom and scroll graphs using the wheel mouse and middle mouse button. Source code and executable are available at: http://lancelot.bio.cornell.edu/jason/presto.html Thanks, J. D. Gans Shalloway Group Cornell University From chemistry-request@server.ccl.net Fri Mar 1 16:42:30 2002 Received: from mserver.wlu.ca ([192.54.242.16]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g21LgU525930 for ; Fri, 1 Mar 2002 16:42:30 -0500 Received: from dgoussev ([192.219.240.167]) by mserver.wlu.ca (8.10.1/8.10.1) with SMTP id g21Lfvf26967 for ; Fri, 1 Mar 2002 16:41:57 -0500 (EST) Message-ID: <007801c1c172$53e120e0$a7f0dbc0@wlu.ca> From: "Dmitri Goussev $Gusev$" To: Subject: zero-point energy correction Date: Fri, 1 Mar 2002 16:42:11 -0600 MIME-Version: 1.0 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Dear Friends: It is my understanding that electronic energies from good (or high) quality QM calculations are usually modified by addition of zero-point energies, for example, to compare two isomers. I believe that zero-point energies are normally obtained from relatively low-quality (for both theory and basis) frequency calculations. This makes sense only if zero-point energies (unlike the electronic ones) are not critically influenced by the quality of the calculation. Is this true? Thanks! Dmitri Goussev (Gusev), Associate Professor Chemistry Department Wilfrid Laurier University Waterloo, Ontario Canada N2L 3C5 Voice: (519) 884-1970, ext. 2736 Fax: (519) 746-0677 E-mail: dgoussev@wlu.ca From chemistry-request@server.ccl.net Fri Mar 1 17:07:51 2002 Received: from front1.chartermi.net ([24.213.60.123]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g21M7p526643 for ; Fri, 1 Mar 2002 17:07:51 -0500 Received: from [24.247.80.10] (HELO hppav) by front1.chartermi.net (CommuniGate Pro SMTP 3.5.3) with SMTP id 65167357; Fri, 01 Mar 2002 17:07:19 -0500 Message-ID: <002e01c1c16d$74c13660$0201a8c0@hppav> From: "Jim Kress" To: "weizhuang" , References: <200203012019.g21KJne914284275@mail.rochester.edu> Subject: Re: CCL:add solvent molecules explictly to the system in TINKER Date: Fri, 1 Mar 2002 17:07:19 -0500 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 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 I'd try: SOAK Subroutine "soak" takes a currently defined solute system and places it into a solvent box, with removal of any solvent molecules that overlap the solute or: XYZEDIT (15) Soak Current Molecule in Box of Solvent As discussed in the Tinker User Guide. Jim ----- Original Message ----- From: "weizhuang" To: Sent: Friday, March 01, 2002 3:30 PM Subject: CCL:add solvent molecules explictly to the system in TINKER > Hi,guys: > > I am studying a organic molecule with TINKER, and I want to add chloroform > molecules around it as solvent. ( ie. put this molecule in the cell and fill > in the rest space of this cell with chloroform molecules ). could anybody > give me some suggestion? > > regards > > wei > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > From chemistry-request@server.ccl.net Fri Mar 1 19:24:14 2002 Received: from relay2.scripps.edu ([137.131.200.30]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g220OE528982 for ; Fri, 1 Mar 2002 19:24:14 -0500 Received: from gamow.scripps.edu (gamow.scripps.edu [137.131.252.67]) by relay2.scripps.edu (8.11.6/TSRI-4.1.1r) with ESMTP id g220Nee15739 for ; Fri, 1 Mar 2002 16:23:40 -0800 (PST) Received: (from case@localhost) by gamow.scripps.edu (8.9.2/TSRI-3.0.1) id QAA135831 for chemistry@ccl.net; Fri, 1 Mar 2002 16:23:39 -0800 (PST) Date: Fri, 1 Mar 2002 16:23:39 -0800 (PST) From: David Case Message-Id: <200203020023.QAA135831@gamow.scripps.edu> To: chemistry@ccl.net Subject: Release of Amber, version 7 Amber 7 released March 1, 2002 It gives us great pleasure to announce the availability of Amber 7, a software package that implements a variety of molecular simulation-based research techniques. The key new features of this release are listed below. We hope these inspire you to license it. Funds for licensing Amber 7 go to support further research by authors of the program; by licensing the program, you are supporting such research. The academic price for licensing is the same as for Amber 6, $400. (This fee may be reduced or waived in special circumstances.) The industrial price is $20,000 for new licensees and $15,000 for those who have licensed Amber 6. To proceed with ordering Amber 7, please follow the instructions at: http://www.amber.ucsf.edu/amber ------------------------------------------------------------------------------- Amber is the collective name for a suite of programs that allow users to carry out molecular dynamics simulations, particularly on biomolecules. None of the individual programs carries this name, but the various parts work reasonably well together, and provide a powerful framework for many common calculations. The term "Amber" is also sometimes used to refer to the empirical force fields that are implemented in the code. It should be recognized however, that the code and force field are separate: several other computer packages have implemented the Amber force fields, and other force fields can be implemented with the Amber programs. Further, the force fields are in the public domain, whereas the codes are distributed under a license agreement. Peter Kollman, who had inspired and led Amber development for more than two decades, died unexpectedly in May 2001. But many of the items cited below (particularly in force field development) were very near completion at the time of his death, and represent the culmination of several years of effort > from both Peter and his collaborators. The Amber development team is committed to continuing to update and improve the software and force fields, and we dedicate Amber 7 to Peter's memory. ------------------------------------------------------------------------------- Amber 7 (2002) represents a significant change from the current version, Amber 6, which was released in December, 1999. Briefly, the major differences include: (1) Several new force fields are available for proteins and nucleic acids. These include versions with polarizable dipoles on atoms, and off-center charges (also called "extra points", and analogous to lone pairs). Amber now provides direct support for TIP3P, TIP4P, TIP5P, SPC/E and POL3 models of water, as well as providing models for chloroform and other organic solvents. (2) A new "general amber force field" that should be applicable to most organic molecules. The automated code to prepare Amber input files using this force field is a new module, called Antechamber. In most cases, Antechamber can directly convert three-dimensional models into files appropriate for molecular mechanics calculations, automatically assigning atom types, charges and force field parameters. (3) Implementation of three new variants of the generalized Born (GB) code, including one that appears to provide a better energy balance between surface-exposed and buried atoms. (4) More efficient PME simulations, with better performance on both single-processor and parallel machines. (5) Updated scripts for MM_PBSA analysis, making input easier to create and providing more options for analysis of the results. (6) Free energy calculations using the thermodynamic integration method can now be carried out in sander. Many investigations that used to require gibbs can now be carried out in a simpler fashion, and free energy studies using the GB model or "extra points" force fields (which are not supported with gibbs) can now be undertaken. (7) New types of restraint forces can be defined that are based on RMS superpositions to reference structures. This "targeted MD" capability can be used to enhance or guide conformational sampling. AMBER authors: David A. Case, David A. Pearlman, James W. Caldwell, Thomas E. Cheatham III, Junmei Wang, Wilson S. Ross, Carlos Simmerling, Tom Darden, Kenneth M. Merz, Robert V. Stanton, Ailan Cheng, James J. Vincent, Mike Crowley, Vickie Tsui, Holger Gohlke, Randall Radmer, Yong Duan, Jed Pitera, Irina Massova, George L. Seibel, U. Chandra Singh, Paul Weiner, and Peter A. Kollman