From chemistry-request@server.ccl.net Fri Jan 26 04:02:07 2001 Received: from hermes.bmc.uu.se (hermes.bmc.uu.se [130.238.39.159]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0Q926w14774 for ; Fri, 26 Jan 2001 04:02:06 -0500 Received: from alpha2.bmc.uu.se ([130.238.37.65]) by hermes.bmc.uu.se (Post.Office MTA v3.5.3 release 223 ID# 0-62649U1500L1000S0V35) with SMTP id se; Fri, 26 Jan 2001 10:03:24 +0100 Received: from werkman.bmc.uu.se by alpha2.bmc.uu.se (5.65v3.2/1.1.10.5/07Jan00-1145AM) id AA23275; Fri, 26 Jan 2001 10:02:04 +0100 Date: Fri, 26 Jan 2001 10:02:03 +0100 (CET) From: David van der Spoel X-Sender: spoel@werkman.bmc.uu.se To: Renxiao Wang Cc: "Dr. Renxiao Wang" Subject: Re: CCL:Solvate organic molecules? In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 25 Jan 2001, Renxiao Wang wrote: >For some reasons we need to solvate organic molecules or even proteins >with explicit water molecules. Will anybody recommend a reliable algorithm >for doing this? It will be ideal if it is able to reproduce the 'real' >situations. The first layer of water is enough. > >Please note that we prefer an algorithm rather than a certain program. It >is simply because we are writing programs in our approach. We certainly >know about some programs, such as AMBER and CHARMm, which can place waters >around a given molecule. But we are a little bit skeptical for what they >generate on the screen. If this makes you skeptical, then try quantum mechanics or X-ray crystallography instead. Writing a program in "your own approach" will certainly not improve the result unless you use a better description than molecular mechanics (i.e. quantum chemistry). Groeten, David. ________________________________________________________________________ Dr. David van der Spoel Biomedical center, Dept. of Biochemistry s-mail: Husargatan 3, Box 576, 75123 Uppsala, Sweden e-mail: spoel@xray.bmc.uu.se www: http://zorn.bmc.uu.se/~spoel phone: 46 18 471 4205 fax: 46 18 511 755 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From chemistry-request@server.ccl.net Fri Jan 26 07:17:17 2001 Received: from gip.u-picardie.fr (gip.u-picardie.fr [193.49.184.17]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0QCHHw16537 for ; Fri, 26 Jan 2001 07:17:17 -0500 Received: from labo5 (labo5.sa.u-picardie.fr [195.83.150.83]) by gip.u-picardie.fr (8.9.3/8.9.3) with SMTP id NAA31906; Fri, 26 Jan 2001 13:16:55 +0100 Date: Fri, 26 Jan 2001 13:16:55 +0100 Message-Id: <200101261216.NAA31906@gip.u-picardie.fr> X-Sender: fyd-phar@mailx.u-picardie.fr X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: amber@cgl.ucsf.edu From: Francois Dupradeau Subject: MEP with GAMESS or GAUSSIAN Cc: chemistry@ccl.net Dear All, I got molecular electrostatic potential (MEP) for an optimized model using GAMESS (based on the Connolly surface) in order to develop RESP charges. Unfortunately, the RESP charges obtained from the GAMESS MEP are different > from the published RESP charges (MEP obtained with GAUSSIAN). Does someone meet this problem ? For me, it seems to depend on the molecule orientation of the OPTIMIZED structure. I know that such problem was reported for CHELP/GAMESS (Woods et al. J Comput Chem 1990). Is there the same problem with the Connolly surface ? Is there a way to get highly similar RESP charges with GAMESS/RESP than those obtained with GAUSSIAN/RESP ? Thanks a lot, Best regards, Francois -- F.-Y. Dupradeau http://www.u-picardie.fr/UPIC/UPJV/recherche/labos/bpd/fyd.htm From chemistry-request@server.ccl.net Fri Jan 26 00:57:58 2001 Received: from hotmail.com (f248.law8.hotmail.com [216.33.241.248]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0Q5vww14035 for ; Fri, 26 Jan 2001 00:57:58 -0500 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Thu, 25 Jan 2001 21:55:58 -0800 Received: from 134.129.118.146 by lw8fd.law8.hotmail.msn.com with HTTP; Fri, 26 Jan 2001 05:55:58 GMT X-Originating-IP: [134.129.118.146] From: "xin hu" To: chemistry@ccl.net Subject: help for Kollman chargesI Date: Fri, 26 Jan 2001 05:55:58 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 26 Jan 2001 05:55:58.0899 (UTC) FILETIME=[A7D6D830:01C0875C] Dear CCLers: I need the Kollman united atom charges of deprotonated histidine(histidinate) and the unprotonated form of Glu. would you please let me know the charges because I could not get the charges > from the AMBER6.0. BTW, besides the sybyl and amber4.0(?), is there any other software can calculate the Kollman charges? Thanks for your help. ---------------------------------------------------------- Xin Hu Department of Pharmaceutical Sciences College of Pharmacy North Dakota State University Fargo, ND 58105 Tel: 701-231-8298(office) 701-231-4193(home) 701-231-7781(Fax) E-mail: xin_hu@ndsu.nodak.edu xxh0541@hotmail.com Mail address: 236 E Court University Village Fargo, ND 58102 ---------------------------------------------------------- _________________________________________________________________ Get your FREE download of MSN Explorer at http://explorer.msn.com From chemistry-request@server.ccl.net Fri Jan 26 10:03:02 2001 Received: from mtiwmhc23.worldnet.att.net (mtiwmhc23.worldnet.att.net [204.127.131.48]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0QF2nw17211 for ; Fri, 26 Jan 2001 10:03:01 -0500 Received: from daveg.fsba.com ([12.73.128.46]) by mtiwmhc23.worldnet.att.net (InterMail vM.4.01.03.10 201-229-121-110) with ESMTP id <20010126150116.YWVX28450.mtiwmhc23.worldnet.att.net@daveg.fsba.com>; Fri, 26 Jan 2001 15:01:16 +0000 Message-Id: <5.0.2.1.0.20010126065241.028cdde0@12.17.172.66> X-Sender: davidgallagher@12.17.172.66 (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 5.0.2 Date: Fri, 26 Jan 2001 07:02:42 -0800 To: Maija Lahtela From: David Gallagher Subject: Re: Visualization of double and triple bonds Cc: chemistry@ccl.net In-Reply-To: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed CAChe does this and it also has special renderings for ionic, weak, coordinate and pi bonds. CAChe can also show calculated or formal bond order by diameter and color of a single cylinder. You can download a free evaluation copy at http://www.cachesoftware.com/ David Gallagher, Fujitsu At 03:31 PM 1/22/01 +0200, Maija Lahtela wrote: >Dear CCLers, > >I would like to >know if there are molecular modeling program such as RasMol, >WebLAbviewer that could present double bond as two tubes and triple bond >with three tubes ( the way as student are used books of chemistry in high >school or collage). > >Yours, >Maija L.-K. > >***************************************************** >Maija Lahtela-Kakkonen, Researcher >CSC-Scientific Computing >Tekniikantie 15 a D, P.O.Box 405 >FIN-02101 ESPOO FINLAND >TEL 358-9-4572079 /050-3819506, FAX 358-9-4572302 >E-MAIL mlahtela@csc.fi, Internet:www.csc.fi >**************************************************** From chemistry-request@server.ccl.net Fri Jan 26 10:55:20 2001 Received: from ncsbex78.ncsbe.jnj.com (smtp.be.jnj.com [194.74.108.12]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0QFtJw17476 for ; Fri, 26 Jan 2001 10:55:20 -0500 Received: from smtp.jnj.com by smtp.jnj.com id f0QFtJT01440; Fri, 26 Jan 2001 16:55:19 +0100 (MET) Received: FROM ncsbebeexh3.ncsbe.jnj.com BY ncsbebesvc06.jnjeu.jnj.com ; Fri Jan 26 16:55:18 2001 +0100 Received: by ncsbebeexh3.ncsbe.jnj.com with Internet Mail Service (5.5.2651.58) id ; Fri, 26 Jan 2001 16:55:17 +0100 Message-ID: <3C843A61C1C6D4119E0A0008C7242D3ED33F3C@JANBEBEEXS3.janbe.jnj.com> From: "Bultinck, Patrick [JanBe Extern]" To: "'chemistry@ccl.net'" Subject: RE: MEP with GAMESS or GAUSSIAN Date: Fri, 26 Jan 2001 16:55:13 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2651.58) Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C087B0.5E461920" 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_01C087B0.5E461920 Content-Type: text/plain; charset="iso-8859-1" Different parameters may play a role : GAMESS keyword Gaussian keyword - Number of layers see LAYER in $PDC IOp(6/41) - Density of points on layer see PTDENS in $PDC IOp(6/42) - Increment between layers see VDWINC in $PDC IOp(6/43) - vdW scale factor for 1st layer see VDWSCL in $PDC IOp(6/56) but added this one myself :-) If you would take the points from GAMESS (standard provided by GAMESS), and insert them into G98, take care in symmetry, use NoSymm, I would say. Maybe using the same parameters in both programs, you might still want to check if the same points are being used on some surface (CONNOLLY). Gamess does this happily, G98 only if providing some overlay options (but again, added some myself for extra flexibility in G98). Also make a note what multipoles you are constraining in both molecules, just total charge, or dipole as well, or quadrupole maybe. You can almost perfectly reproduce things between the two programs (see also source file prplib.src of GAMESS where this is also mentionned), if you 'play' around with the options, making sure you are doing the same thing in both programs... Hope this might help a little (sorry for sending this to the entire list, I lost the original mail, and had this reply lying about, forgetting to send it. Maybe it is still of help to the original sender !) Kind regards, Patrick Bultinck Ghent University Belgium ------_=_NextPart_001_01C087B0.5E461920 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable RE: MEP with GAMESS or GAUSSIAN

Different parameters may play a role :
        =         =         =         =         GAMESS = keyword          Gaussian = keyword
- Number of layers      =         see LAYER in = $PDC       =         IOp(6/41)
- Density of points on layer    see = PTDENS in $PDC      IOp(6/42)
- Increment between = layers      see VDWINC in = $PDC      IOp(6/43)
- vdW scale factor for 1st layer
        =         =         =         =         see VDWSCL in = $PDC      IOp(6/56) but added this one myself = :-)

If you would take the points from GAMESS (standard = provided by GAMESS), and insert them into G98, take care in symmetry, = use NoSymm, I would say. Maybe using the same parameters in both = programs, you might still want to check if the same points are being = used on some surface (CONNOLLY). Gamess does this happily, G98 only if = providing some overlay options (but again, added some myself for extra = flexibility in G98). Also make a note what multipoles you are = constraining in both molecules, just total charge, or dipole as well, = or quadrupole maybe.

You can almost perfectly reproduce things between the = two programs (see also source file prplib.src of GAMESS where this is = also mentionned), if you 'play' around with the options, making sure = you are doing the same thing in both programs...

Hope this might help a little (sorry for sending this = to the entire list, I lost the original mail, and had this reply lying = about, forgetting to send it. Maybe it is still of help to the original = sender !)

Kind regards,

Patrick Bultinck
Ghent University
Belgium

------_=_NextPart_001_01C087B0.5E461920-- From chemistry-request@server.ccl.net Fri Jan 26 12:27:15 2001 Received: from gpo.cam.msi-eu.com (cam.msi-eu.com [192.190.183.254]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0QHREw18027 for ; Fri, 26 Jan 2001 12:27:15 -0500 Received: from bonanza (dhcp139.cam.msi-eu.com [172.27.65.139]) by gpo.cam.msi-eu.com (8.9.3/8.9.3/Debian 8.9.3-21) with ESMTP id RAA00834; Fri, 26 Jan 2001 17:25:10 GMT X-Authentication-Warning: gpo.cam.msi-eu.com: Host dhcp139.cam.msi-eu.com [172.27.65.139] claimed to be bonanza Message-Id: <4.2.2.20010126163745.00ba3980@mailhost.cam.msi-eu.com> X-Sender: phil_hastings@mailhost.cam.msi-eu.com X-Mailer: QUALCOMM Windows Eudora Pro Version 4.2.2 Date: Fri, 26 Jan 2001 17:24:52 +0000 To: Maija Lahtela From: Phil Hastings Subject: Re: CCL:Visualization of double and triple bonds Cc: chemistry@ccl.net In-Reply-To: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Materials Visualizer (core module of Materials Studio, the new PC-based package from MSI), has a versatile range of options for graphical display of bond order, including what you describe below. It can handle single, resonant, double, triple and pi-bonds. Bond order can be easily defined via the various sketching and editing options, and there is also a bond calculation tool. If you'd like further information I'd recommend visiting www.materials-studio.com You will also see a link there to order an evaluation copy. Sincerely Phil Hastings, MSI At 03:31 PM 1/22/01 +0200, you wrote: >Dear CCLers, > >I would like to >know if there are molecular modeling program such as RasMol, >WebLAbviewer that could present double bond as two tubes and triple bond >with three tubes ( the way as student are used books of chemistry in high >school or collage). > >Yours, >Maija L.-K. > >***************************************************** >Maija Lahtela-Kakkonen, Researcher >CSC-Scientific Computing >Tekniikantie 15 a D, P.O.Box 405 >FIN-02101 ESPOO FINLAND >TEL 358-9-4572079 /050-3819506, FAX 358-9-4572302 >E-MAIL mlahtela@csc.fi, Internet:www.csc.fi >**************************************************** > > > >-= 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 Jan 26 12:34:58 2001 Received: from mail.rpi.edu (root@mail.rpi.edu [128.113.100.7]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0QHYww18113 for ; Fri, 26 Jan 2001 12:34:58 -0500 Received: from curtp5 (curtp5.chem.rpi.edu [128.113.21.59]) by mail.rpi.edu (8.9.3/8.9.3) with SMTP id MAA661570; Fri, 26 Jan 2001 12:34:25 -0500 Message-ID: <3A71B4BC.3E7A@rpi.edu> Date: Fri, 26 Jan 2001 12:32:44 -0500 From: "Curt M. Breneman" Reply-To: brenec@rpi.edu Organization: RPI Department of Chemistry X-Mailer: Mozilla 3.02 (WinNT; I) MIME-Version: 1.0 To: Francois Dupradeau CC: amber@cgl.ucsf.edu, chemistry@ccl.net Subject: Re: CCL:MEP with GAMESS or GAUSSIAN References: <200101261216.NAA31906@gip.u-picardie.fr> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Francois Dupradeau wrote: > > Dear All, > > I got molecular electrostatic potential (MEP) for an optimized model using > GAMESS (based on the Connolly surface) in order to develop RESP charges. > Unfortunately, the RESP charges obtained from the GAMESS MEP are different > > from the published RESP charges (MEP obtained with GAUSSIAN). > Does someone meet this problem ? > > For me, it seems to depend on the molecule orientation of the OPTIMIZED > structure. I know that such problem was reported for CHELP/GAMESS (Woods et > al. J Comput Chem 1990). > Is there the same problem with the Connolly surface ? > > Is there a way to get highly similar RESP charges with GAMESS/RESP than > those obtained with GAUSSIAN/RESP ? > > Thanks a lot, > Best regards, > Francois > -- > F.-Y. Dupradeau > http://www.u-picardie.fr/UPIC/UPJV/recherche/labos/bpd/fyd.htm > Folks, This was the motivation for utilizing a higher point densities and using a different sampling strategy in the CHELPG routine that's implemented in Gaussian9x. See: Breneman, C.M. and Wiberg, K.B., "Determining Atom-Centered Monopoles > from Molecular Electrostatic Potentials. The Need for High Sampling Density in Formamide Conformational Analysis",J. Comp. Chem., 1990,11(3), p. 361-373. Curt Breneman RPI Chemistry From chemistry-request@server.ccl.net Fri Jan 26 13:30:51 2001 Received: from mail.chem.tamu.edu (mail.chem.tamu.edu [165.91.176.8]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0QIUpw18453 for ; Fri, 26 Jan 2001 13:30:51 -0500 Received: from mail.chem.tamu.edu ([165.91.177.32]) by mail.chem.tamu.edu (Post.Office MTA v3.5.3 release 223 ID# 0-64333U1000L100S0V35) with ESMTP id edu for ; Fri, 26 Jan 2001 12:42:03 -0600 Sender: yubo@ccl.net Message-ID: <3A71C2CA.7A6EA134@mail.chem.tamu.edu> Date: Fri, 26 Jan 2001 18:32:42 +0000 From: Yubo Fan Organization: Chemistry Department, Texas A&M University X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP28) X-Accept-Language: zh-CN, en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: Reflect structures throught a plane Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, everyone, I builts molecular structures by Cerius2. After I build a structure, I want to get its enatiomeric structure. But I don't know how to transform it in Cerius2. Could anyone give me advice? Thanks in advance Y. Fan -- ============================================================ Dr. Yubo Fan Email: yubofan@mail.chem.tamu.edu Department of Chemistry Tel: 1-979-845-7222 Texas A&M University College Station, TX 77843 ============================================================ From chemistry-request@server.ccl.net Fri Jan 26 14:10:57 2001 Received: from server.ttpharma.com (ttpharma.com [206.74.77.186]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0QJAvw18736 for ; Fri, 26 Jan 2001 14:10:57 -0500 Received: from jerome ([192.168.4.24]) by server.ttpharma.com (8.9.3/8.8.7) with SMTP id NAA24332 for ; Fri, 26 Jan 2001 13:17:47 -0600 From: "Jerome Baudry" To: Subject: RE: Reflect structures throught a plane Date: Fri, 26 Jan 2001 14:17:45 -0500 Message-ID: <000701c087cc$aa6e3000$1804a8c0@ttpharma.com> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook CWS, Build 9.0.2416 (9.0.2910.0) Importance: Normal In-Reply-To: <3A71C2CA.7A6EA134@mail.chem.tamu.edu> X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 Hi Yubo You can do it manualy and individually for each chiral center: i) Load your molecule in C2 visualizer. Open the 3D-sketcher (Visualizer -> Buil -> 3D sketcher) ii) on the 3D sketcher windows that pops-up, select the 'invert' icon (bottom-right column) iii) now click on the molecule's chiral center(s) you want to invert you should have the molecule updated in the visualizer ***************************************** Jerome Baudry, Ph.D. Research Scientist, Computational Chemistry TransTech Pharma, Inc. 4170 Mendenhall Oaks Pwky, Suite 110 High Point, NC, 27265 http://www.ttpharma.com jbaudry@ttpharma.com tel: (336) 841-0300 #120 fax: (336) 841-0310 > -----Original Message----- > From: Computational Chemistry List > [mailto:chemistry-request@ccl.net]On > Behalf Of Yubo Fan > Sent: Friday, January 26, 2001 1:33 PM > To: CHEMISTRY@ccl.net > Subject: CCL:Reflect structures throught a plane > > > Hi, everyone, > > I builts molecular structures by Cerius2. After I build a structure, I > want to get its enatiomeric structure. But I don't know how > to transform > it in Cerius2. Could anyone give me advice? > > Thanks in advance > > Y. Fan > > -- > ============================================================ > Dr. Yubo Fan Email: yubofan@mail.chem.tamu.edu > Department of Chemistry Tel: 1-979-845-7222 > Texas A&M University > College Station, TX 77843 > ============================================================ > > > > > -= 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 Jan 26 17:40:43 2001 Received: from comm2.umaryland.edu (comm2.umaryland.edu [134.192.1.13]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0QMehw20089 for ; Fri, 26 Jan 2001 17:40:43 -0500 Received: from umaryland.edu (falcon2.umaryland.edu [134.192.68.11]) by comm2.umaryland.edu (8.9.3/8.9.3) with ESMTP id RAA13400 for ; Fri, 26 Jan 2001 17:40:45 -0500 (EST) Received: from localhost (nbanaval@localhost) by umaryland.edu (8.10.0/8.10.0) with ESMTP id f0QMXIZ24509 for ; Fri, 26 Jan 2001 17:33:18 -0500 (EST) Date: Fri, 26 Jan 2001 17:33:18 -0500 (EST) From: Nilesh Banavali To: chemistry@ccl.net Subject: Summary of responses for WHAM question Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi CCLers, Here is a belated summary for the WHAM programs available and comments regarding possible differences amongst them. Thanks to Jerome Baudry and Konrad Hinsen for their help. Serge Crouzy and Konrad Hinsen have their own WHAM programs. 'As for possible differences in the results, I would first check the default values for all the WHAM parameters. In particular, the number of iterations of the WHAM equations was found to significantly affect the convergence of the results (see following paper by Crouzy et al.). Also, in the case of a periodic degree of freedom, like e.g. a dihedral angle, the final results would be changed if you correct the hysteresis (by, for instance, replicating times series at the ends of the reaction coordinate, or by imposing equality of the PMF values at both ends of the reaction coordinate during the WHAM iterations)' - Jerome Baudry 'There could be minor differences due to different criteria for terminating the iterations etc. These differences could become important when the data is insufficient (e.g. no sufficient overlap between neighbouring windows)' - Konrad Hinsen References Efficient calculation of 2-dimensional adiabatic and free energy maps: Application to the isomerization of the C13=C14 and C15=N16 bonds in the retinal of bacteriorhodopsin. Serge Crouzy, Jerome Baudry, Jeremy C. Smith and Benoit Roux. J. Comp. Chem. 20,15 (1999) 1644-1658. Justin Gullingsrud, Rosemary Braun, and Klaus Schulten. Reconstructing potentials of mean force through time series analysis of steered molecular dynamics simulations. Journal of Computational Physics, 151:190--211, 1999. ( see this paper at: http://www.ks.uiuc.edu/Publications/Papers/abstract.cgi?tbcode=GULL99 ) O. Roche, K. Hinsen, M.J. Field Theoretical study of the conformation of the H-protein lipoamide arm as a function of the terminal group Proteins 36(2), 228 (1999) Thanks, Nilesh Banavali Graduate Student, University of Maryland. From chemistry-request@server.ccl.net Fri Jan 26 16:40:42 2001 Received: from web1106.mail.yahoo.com (web1106.mail.yahoo.com [128.11.23.126]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f0QLegw19823 for ; Fri, 26 Jan 2001 16:40:42 -0500 Received: (qmail 21345 invoked by uid 60001); 26 Jan 2001 21:40:42 -0000 Message-ID: <20010126214042.21344.qmail@web1106.mail.yahoo.com> Received: from [129.15.12.147] by web1106.mail.yahoo.com; Fri, 26 Jan 2001 13:40:42 PST Date: Fri, 26 Jan 2001 13:40:42 -0800 (PST) From: Adam Hixson Reply-To: chixson@chemdept.chem.ou.edu Subject: SHAKE and the MCE. To: CHEMISTRY@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii I just read one of the original accounts of the SHAKE algorythm (J Comp Phys 1977 23 327-41), and I have a question about the energy produced. To what extent does a microcannonical ensemble simulation using SHAKE conserve the energy? The authors of the above paper mentioned that it fluxuated about a stable value, but gave no indication as to how great the flux was. Anybody know anything about this? Thanks. ===== ---- Adam Hixson Department of Chemistry and Biochemistry The University of Oklahoma chixson@chemdept.chem.ou.edu 620 Parrington Oval hixsonc@yahoo.com Norman, OK 73069 __________________________________________________ Do You Yahoo!? Yahoo! Auctions - Buy the things you want at great prices. http://auctions.yahoo.com/ From chemistry-request@server.ccl.net Fri Jan 26 18:23:06 2001 Received: from femail12.sdc1.sfba.home.com (femail12.sdc1.sfba.home.com [24.0.95.108]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0QNN5w20308 for ; Fri, 26 Jan 2001 18:23:05 -0500 Received: from C1353359A ([65.4.172.51]) by femail12.sdc1.sfba.home.com (InterMail vM.4.01.03.00 201-229-121) with SMTP id <20010126232300.QNMT24800.femail12.sdc1.sfba.home.com@C1353359A>; Fri, 26 Jan 2001 15:23:00 -0800 Message-ID: <000e01c087ee$487b24d0$33ac0441@sttln1.wa.home.com> From: "Mark A. Thompson" To: "env chem" , "organic chem" , "nat prod" , "GAMESS" , "chem web" , "CCL" , "chem ed2" , "chem ed" Subject: ArgusLab 2.0 final release available Date: Fri, 26 Jan 2001 15:18:24 -0800 ArgusLab 2.0 final release is available! ArgusLab is still free. The new website is: http://www.planaria-software.com In addition to the features listed below, I added calculating rotary strengths to this release. There were numerous bug fixes, additions to the help system, and restart from prior SCF added to the calculation dialog boxes. enjoy Mark Thompson, President Planaria Software Seattle, WA. ArgusLab is a molecular modeling program for Microsoft Windows operating systems. Overview of 2.0 features: ----------------------------- 1. Interactive 3D Molecule Builder with: Interactive 3D manipulator Fragment Library Beautify Geometry Automatically Add/Hide/Delete Hydrogens Cut & Paste Supports Multiple-Level Undo/Redo. Multiple Rendering Styles for Atoms and Bonds Geometry Monitors 2. Calculation Types Single-Point Energies Optimize Geometries Electronic Excitation Spectra Self Consistent Reaction Field (SCRF) Solvent Model for Electronic Spectra 3. Molecular Mechanics Universal Force Field (UFF) for the entire periodic table 4. Quantum Mechanics Extended Huckel for entire periodic table MNDO, AM1, and PM3 semi-empirical Hamiltonians INDO1/s semi-empirical Hamiltonian Restricted and Unrestricted Hartree-Fock SCF 5. File Types: supports XYZ, PDB, and ArgusLab XML file formats. 6. HTML Help 7. No size limitations for molecules or calculations other than available system resources 8. Multi-threaded architecture allows multiple molecules opened simultaneously and running calculations 9. Runs on Windows 95/98, Windows NT 4.0, Windows 2000