From shenkin@sbu.ac.uk Tue Mar 26 17:18:56 1996 Received: from psb.sbu.ac.uk for shenkin@sbu.ac.uk by www.ccl.net (8.7.1/950822.1) id QAA23041; Tue, 26 Mar 1996 16:56:30 -0500 (EST) From: Received: from HYDRA (BIG::SYSTEM) by PSB (MX V4.2 VAX) with SMTP (DECnet); Tue, 26 Mar 1996 21:56:46 GMT Received: by vax.sbu.ac.uk (MX V4.2 VAX) with SITE; Tue, 26 Mar 1996 21:52:41 GMT Received: by vax.sbu.ac.uk (MX V4.2 VAX) with SITE; Tue, 26 Mar 1996 19:00:59 GMT Received: from PSB (PSB::SYSTEM) by BIG (MX V4.1 VAX) with SMTP (DECnet); Sat, 16 Mar 1996 04:45:20 GMT Received: from www.ccl.net by psb.sbu.ac.uk (MX V4.1 VAX) with SMTP; Sat, 16 Mar 1996 02:42:39 GMT Received: for chemistry-request@www.ccl.net by www.ccl.net (8.7.1/950822.1) id VAA01510; Fri, 15 Mar 1996 21:17:00 -0500 (EST) Received: from mailhub.cc.columbia.edu for shenkin@still3.chem.columbia.edu by www.ccl.net (8.7.1/950822.1) id VAA01423; Fri, 15 Mar 1996 21:12:05 -0500 (EST) Received: from still3.chem.columbia.edu (still3.chem.columbia.edu [128.59.112.36]) by mailhub.cc.columbia.edu (8.7.3/8.7.3) with SMTP id VAA18441; Fri, 15 Mar 1996 21:11:53 -0500 (EST) Received: by still3.chem.columbia.edu (931110.SGI/930416.SGI.AUTO) for @mailhub.cc.columbia.edu:jsalb@ix.netcom.com id AA09497; Fri, 15 Mar 96 21:11:53 -0500 Date: Fri, 15 Mar 96 21:11:53 -0500 Originally-From: Message-ID: <9603160211.AA09497@still3.chem.columbia.edu> To: chemistry@www.ccl.net, jsalb@ix.netcom.com (Jesse Salb) Subject: CCL:Pronunciation of "Conformer" We have been having some major problems with our mail system for the last week. The backlog is now being cleared. However you may receive messages more than once. Our apologies for any inconvenience caused. =============================== Original Message follows ====================== > From chemistry-request@www.ccl.net Fri Mar 15 21:06:09 1996 > I apologize for wasting valuable bandwidth, but is the preferred > pronunciation of "conformer" either "con' form er" > or "con form' er"? If you say "con' form er" you'll be a "con form' er" to common usage. -P. **************** In Memorium, Minnie Pearl, 1913-1996, RIP ***************** *** Peter S. Shenkin, Box 768 Havemeyer Hall, Chemistry, Columbia Univ., *** *** NY, NY 10027; shenkin@columbia.edu; (212)854-5143; FAX: 678-9039 *** *** MacroModel home page: www.cc.columbia.edu/cu/chemistry/mmod/mmod.html*** -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: shenkin@still3.chem.columbia.edu -- Original Sender From: Address: shenkin@still3.chem.columbia.edu CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search Web: http://www.ccl.net/chemistry.html From jsalb@sbu.ac.uk Tue Mar 26 20:09:16 1996 Received: from psb.sbu.ac.uk for jsalb@sbu.ac.uk by www.ccl.net (8.7.1/950822.1) id SAA24242; Tue, 26 Mar 1996 18:38:47 -0500 (EST) From: Received: from BIG (BIG::SYSTEM) by PSB (MX V4.2 VAX) with SMTP (DECnet); Tue, 26 Mar 1996 23:39:04 GMT Received: by vax.sbu.ac.uk (MX V4.2 VAX) with SITE; Tue, 26 Mar 1996 23:35:51 GMT Received: by vax.sbu.ac.uk (MX V4.2 VAX) with SITE; Tue, 26 Mar 1996 23:31:45 GMT Received: from PSB (PSB::SYSTEM) by BIG (MX V4.1 VAX) with SMTP (DECnet); Sat, 16 Mar 1996 04:13:40 GMT Received: from www.ccl.net by psb.sbu.ac.uk (MX V4.1 VAX) with SMTP; Sat, 16 Mar 1996 01:40:56 GMT Received: for chemistry-request@www.ccl.net by www.ccl.net (8.7.1/950822.1) id UAA00728; Fri, 15 Mar 1996 20:19:01 -0500 (EST) Received: from ix3.ix.netcom.com for jsalb@ix.netcom.com by www.ccl.net (8.7.1/950822.1) id TAA00612; Fri, 15 Mar 1996 19:44:05 -0500 (EST) Received: from lax-ca25-28.ix.netcom.com by ix3.ix.netcom.com (8.6.13/SMI-4.1/Netcom) id QAA29338; Fri, 15 Mar 1996 16:43:37 -0800 Originally-From: To: chemistry@www.ccl.net Subject: CCL:Pronunciation of "Conformer" Date: Sat, 16 Mar 1996 00:43:36 GMT Message-ID: <314a0e15.34336363@smtp.ix.netcom.com> We have been having some major problems with our mail system for the last week. The backlog is now being cleared. However you may receive messages more than once. Our apologies for any inconvenience caused. =============================== Original Message follows ====================== I apologize for wasting valuable bandwidth, but is the preferred pronunciation of "conformer" either "con' form er" or "con form' er"? Thanks. -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: jsalb@ix.netcom.com -- Original Sender From: Address: jsalb@ix.netcom.com CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search Web: http://www.ccl.net/chemistry.html From p.grootenhuis@sbu.ac.uk Tue Mar 26 20:09:21 1996 Received: from psb.sbu.ac.uk for p.grootenhuis@sbu.ac.uk by www.ccl.net (8.7.1/950822.1) id TAA24397; Tue, 26 Mar 1996 19:07:12 -0500 (EST) From: Received: from HYDRA (BIG::SYSTEM) by PSB (MX V4.2 VAX) with SMTP (DECnet); Wed, 27 Mar 1996 00:07:30 GMT Received: by vax.sbu.ac.uk (MX V4.2 VAX) with SITE; Tue, 26 Mar 1996 07:57:03 GMT Received: by vax.sbu.ac.uk (MX V4.2 VAX) with SITE; Tue, 26 Mar 1996 03:05:40 GMT Received: from PSB (PSB::SYSTEM) by BIG (MX V4.1 VAX) with SMTP (DECnet); Sat, 16 Mar 1996 17:04:07 GMT Received: from www.ccl.net by psb.sbu.ac.uk (MX V4.1 VAX) with SMTP; Sat, 16 Mar 1996 02:34:12 GMT Received: for chemistry-request@www.ccl.net by www.ccl.net (8.7.1/950822.1) id VAA01076; Fri, 15 Mar 1996 21:02:40 -0500 (EST) Received: from gatekeeper.oss.akzonobel.nl for p.grootenhuis@organon.akzonobel.nl by www.ccl.net (8.7.1/950822.1) id DAA22328; Tue, 12 Mar 1996 03:30:03 -0500 (EST) Received: (from mail@localhost) by gatekeeper.oss.akzonobel.nl (8.6.12/8.6.12) id JAA03370 for ; Tue, 12 Mar 1996 09:33:15 +0100 Received: from apou01.akzonobel.nl(145.49.90.59) by gatekeeper.oss.akzonobel.nl via smap (V1.3) id sma032068; Tue Mar 12 09:32:56 1996 Received: by apou01.akzonobel.nl (8.7.1/AKZONOBEL-WvdL/951013) id JAA05463; Tue, 12 Mar 1996 09:28:07 GMT Received: (from groot@localhost) by organon.akzonobel.nl (950511.SGI.8.6.12.PATCH526/8.6.12) id JAA08196 for chemistry@www.ccl.net; Tue, 12 Mar 1996 09:29:47 GMT Originally-From: Message-ID: <199603120929.JAA08196@organon.akzonobel.nl> Subject: CCL:MD of non-globular proteins - answers To: chemistry@www.ccl.net Date: Tue, 12 Mar 1996 09:29:44 +0000 (WET) We have been having some major problems with our mail system for the last week. The backlog is now being cleared. However you may receive messages more than once. Our apologies for any inconvenience caused. =============================== Original Message follows ====================== CCL-ers, My original questions concerned MD of non-globular proteins where I observed both in gas-phase and aqueous simulations a rather strong tendency of the system to adopt conformations that result in more globular shapes. Questions: (1) Is anybody aware of (published) MD simulations of non-globular proteins ? (2) Does anybody has (preferably computationally inexpensive) suggestions on how to handle such a system ? Thanks for your suggestions! Here is a summary: ------------------------------------------------------------------------------- From: bear@ellington.pharm.arizona.edu (Soaring Bear) Sounds like you ought to use more gentle methods, like lower temp, ramp gradient, shorter times, higher dielectric. ------------------------------------------------------------------------------- From: Willy Wriggers The problems you mentioned have also been observed by us. We carry out MD simulations of calmodulin, a dumbbell shaped protein of only 148 aa residues, in solution (see "calmodulin" on my homepage at http://www.ks.uiuc.edu/~wriggers/). Earlier simulations by our collaborators at CUNY (see Pascal-Ahuir, Mehler, Weinstein: Molecular Engineering 1, 231-247, 1991 for review) had a limited solvent model (only explicit surface waters) and it could not be ruled out that observed structural changes were caused by the protein "sticking it's tongue out" of the water molecules, which tend to diffuse to the center of the protein. The way we solve the problem now is by placing the protein in a 44 A radius sphere of water, which brings the total system size to 33,000 atoms. Since the explicit solvent model and salt ions slow down the movement of calmodulin's domains, we need to simulate for 3 ns. I know such a calculation may not be feasible in every case. If you have limited resources, it's better to simulate only parts of the protein which are of interest, i.e. use stochastic boundary conditions (Brooks, Karplus, Pettitt: Proteins. (1988) Wiley Interscience Pub.). I would not recommend using a distance-dependent dielectric constant to model the solvent because it gives you the wrong electrostatics. Depending on your problem, you may also want to look at other newer "in vacuo" simulation techniques which use constraints (Collins, Burt, Erickson: Flap opening in HIV-1 protease... (1995) Nature Struct. Biol. 2:334-338). ------------------------------------------------------------------------------- From: alper@netcom.com (Howard Alper) In your simulations, how do you treat the nonbonded interactions. In particular, do you use switching functions? The reason I ask is that while these functions do smooth away discontinuities in the energy, they can create artificial maxima and minima in the interatomic, interresidue, or intermolecular forces that could trap the particles at particular separations from each other. This can be seen by looking at the way the switching function varies in the region where it goes from 1 to 0, and considering what the derivative of the function would look like. I have seen this for simulations of neat water (K. Lau. H. E. Alper, T. Thacher, and T. R. Stouch, J. Phys. Chem. 98, 8785 (1994)), as well as in simulations of lipid bilayer systems. Switching functions can decrease the degree of motion a system undergoes, compared to other cutoff methods... ------------------------------------------------------------------------------- From: Vincent Collura I am not surprised about " a tendency" to fold into a globular (more compact) shape in the gas-phase, the reason is certainly the electrostatics term of the nonbonded energy. The best is to increase the dielectric constant (distance dependent or not in your case?) close to the value of water. In your case, it will be a good approximation because if it is not globular or compact it can be deduced that it has certainly a substantial part of the surface in contact with the solvent unless it is a membrane protein. I am slightly more surprised that you observed this effect with the explicit description of the solvent. Normally it should be more "rigid". If it is not a compact protein ( higher % of hydrophilic residues? Is there a well defined hydrophobic core in your protein ?) it is normal that it undergoes larger average fluctuation at room temperature in the solvent, but it should'nt lead to a more compact protein. Are you using Periodic Box conditions or only a water shell around the protein ? Have a look in the way the electrostatics terms are parameterized in your force field.... ______________________________________________________________________________ Dr. Peter D.J. Grootenhuis | N.V. Organon / CMC Dept. RK2337 | Phone : +31-412-661920 P.O. Box 20 / 5340 BH Oss | Fax : +31-412-662539 The Netherlands | E-mail : p.grootenhuis@organon.akzonobel.nl _________________________________|____________________________________________ --- Administrivia: This message is automatically appended by the mail exploder: CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search Web: http://www.ccl.net/chemistry.html --- From gaussian.com@sbu.ac.uk Tue Mar 26 20:18:55 1996 Received: from psb.sbu.ac.uk for gaussian.com@sbu.ac.uk by www.ccl.net (8.7.1/950822.1) id TAA24568; Tue, 26 Mar 1996 19:54:27 -0500 (EST) From: Received: from HYDRA (BIG::SYSTEM) by PSB (MX V4.2 VAX) with SMTP (DECnet); Wed, 27 Mar 1996 00:54:35 GMT Received: by vax.sbu.ac.uk (MX V4.2 VAX) with SITE; Wed, 27 Mar 1996 00:51:41 GMT Received: by vax.sbu.ac.uk (MX V4.2 VAX) with SITE; Wed, 27 Mar 1996 00:47:10 GMT Received: from PSB (PSB::SYSTEM) by BIG (MX V4.1 VAX) with SMTP (DECnet); Sat, 16 Mar 1996 04:49:11 GMT Received: from www.ccl.net by psb.sbu.ac.uk (MX V4.1 VAX) with SMTP; Fri, 15 Mar 1996 16:58:36 GMT Received: for chemistry-request@www.ccl.net by www.ccl.net (8.7.1/950822.1) id LAA24145; Fri, 15 Mar 1996 11:21:50 -0500 (EST) Received: from relay5.UU.NET for gaussian.com!moses@lorentzian.com by www.ccl.net (8.7.1/950822.1) id LAA24046; Fri, 15 Mar 1996 11:11:42 -0500 (EST) Received: from uucp6.UU.NET by relay5.UU.NET with SMTP id QQahdw24763; Fri, 15 Mar 1996 11:11:38 -0500 (EST) Message-ID: Received: from m10.UUCP by uucp6.UU.NET with UUCP/RMAIL ; Fri, 15 Mar 1996 11:11:40 -0500 Received: by m10.lorentzian.com; Fri, 15 Mar 1996 11:09:12 -0500 Received: by mousse.gaussian.com; Fri, 15 Mar 1996 10:10:15 -0500 Originally-From: Received: from BIG (BIG::SYSTEM) by PSB (MX V4.2 VAX) with SMTP (DECnet); Wed, 27 Mar 1996 01:18:54 GMT Received: by vax.sbu.ac.uk (MX V4.2 VAX) with SITE; Wed, 27 Mar 1996 01:14:48 GMT Received: by vax.sbu.ac.uk (MX V4.2 VAX) with SITE; Wed, 27 Mar 1996 01:06:45 GMT Received: from PSB (PSB::SYSTEM) by BIG (MX V4.1 VAX) with SMTP (DECnet); Sat, 16 Mar 1996 04:58:17 GMT Received: from www.ccl.net by psb.sbu.ac.uk (MX V4.1 VAX) with SMTP; Fri, 15 Mar 1996 19:57:37 GMT Received: for chemistry-request@www.ccl.net by www.ccl.net (8.7.1/950822.1) id OAA27602; Fri, 15 Mar 1996 14:19:48 -0500 (EST) Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id NAA26323; Fri, 15 Mar 1996 13:27:10 -0500 (EST) Received: from gateway.rohmhaas.com for THPierce@rohmhaas.com by bedrock.ccl.net (8.7.1/950822.1) id NAA17282; Fri, 15 Mar 1996 13:27:09 -0500 (EST) Received: from brthp.br.rohmhaas.com by gateway.rohmhaas.com (AIX 3.2/UCB 5.64/4.03) id AA24232; Fri, 15 Mar 1996 13:27:20 -0500 Message-ID: <2.2.32.19960315181723.017e1954@monte.br.rohmhaas.com> Date: Fri, 15 Mar 1996 13:17:23 -0500 To: jpcannady@dcrn.e-mail.com, chemistry@ccl.net Originally-From: Subject: CCL:Intranet Symposium At ACS in Orlando We have been having some major problems with our mail system for the last week. The backlog is now being cleared. However you may receive messages more than once. Our apologies for any inconvenience caused. =============================== Original Message follows ====================== At 12:25 PM 3/15/96 EST, you wrote: >Submission deadline is April 15, 1996 or March 15, 1996 (which is today)? Hmm Good Point. April 15th. The submit today request was added days ago. It was meant to encourage people to act QUICKLY. I forgot that today is the Ides of March. Sorry. . > >ACS Computers and Chemistry Division Call for Papers: > >At Orlando, Florida during ACS 212th National Meeting >August 25-29, 1996 a Symposium on: > >IntraNets: Chemical Applications and Uses of Web technologies >Talks on these topics are solicited. Please send a title and short >description to the session organizers by April 15, 1996, ie Today! >Session Organizers: : >h.rzepa@ic.ac.uk - Prof. Henry Rzepa >smb@smb.chem.niu.edu Prof. Steven Bachrach >THPierce@RohmHaas.Com - Dr. Tom Pierce > ----- Sincerely, Tom Pierce - THPierce@RohmHaas.Com - Computational Chemist "These opinions are those of the writer and not the Rohm and Haas Company." -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: owner-chemistry@ccl.net -- Original Sender From: Address: THPierce@rohmhaas.com CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search Web: http://www.ccl.net/chemistry.html From owner-chemistry@ccl.net Tue Mar 26 21:19:03 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id UAA25543; Tue, 26 Mar 1996 20:57:55 -0500 (EST) Received: from psb.sbu.ac.uk for thpierce@sbu.ac.uk by bedrock.ccl.net (8.7.1/950822.1) id UAA07704; Tue, 26 Mar 1996 20:57:48 -0500 (EST) From: Received: from BIG (BIG::SYSTEM) by PSB (MX V4.2 VAX) with SMTP (DECnet); Wed, 27 Mar 1996 01:57:55 GMT Received: by vax.sbu.ac.uk (MX V4.2 VAX) with SITE; Wed, 27 Mar 1996 01:55:43 GMT Received: by vax.sbu.ac.uk (MX V4.2 VAX) with SITE; Tue, 26 Mar 1996 11:25:12 GMT Received: from PSB (PSB::SYSTEM) by BIG (MX V4.1 VAX) with SMTP (DECnet); Sat, 16 Mar 1996 05:15:37 GMT Received: from www.ccl.net (www.ccl.net) by psb.sbu.ac.uk (MX V4.1 VAX) with SMTP; Fri, 15 Mar 1996 17:34:57 GMT Received: for chemistry-request@www.ccl.net by www.ccl.net (8.7.1/950822.1) id LAA24348; Fri, 15 Mar 1996 11:59:51 -0500 (EST) Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id KAA23534; Fri, 15 Mar 1996 10:20:00 -0500 (EST) Received: from gateway.rohmhaas.com for THPierce@rohmhaas.com by bedrock.ccl.net (8.7.1/950822.1) id KAA11844; Fri, 15 Mar 1996 10:19:58 -0500 (EST) Received: from brthp.br.rohmhaas.com by gateway.rohmhaas.com (AIX 3.2/UCB 5.64/4.03) id AA11500; Fri, 15 Mar 1996 10:20:09 -0500 Message-ID: <2.2.32.19960315151013.0090ed68@monte.br.rohmhaas.com> Date: Fri, 15 Mar 1996 10:10:13 -0500 To: chemistry@ccl.net, CHMINF-L@IUBVM.UCS.INDIANA.EDU Originally-From: Subject: CCL:Intranet Symposium At ACS in Orlando CC: smb@smb.chem.niu.edu, h.rzepa@ic.ac.uk (Rzepa,Henry) We have been having some major problems with our mail system for the last week. The backlog is now being cleared. However you may receive messages more than once. Our apologies for any inconvenience caused. =============================== Original Message follows ====================== ACS Computers and Chemistry Division Call for Papers: At Orlando, Florida during ACS 212th National Meeting August 25-29, 1996 a Symposium on: IntraNets: Chemical Applications and Uses of Web technologies During the Orlando ACS meeting the Computers and Chemistry division is sponsoring a session on Intranets. This session will cover the use of World-Wide Web technologies to solve problems in chemical research and chemical information sharing within an organization. We are planning a concurrrent electronic session as well, including updating our award-giving survey "Best of the Web". Please vote for or submit your "Best Web Chemical Sites" at http://www.ch.ic.ac.uk/infobahn/vote.html and at the bottom of: http://hackberry.chem.niu.edu/Infobahn/Paper38#vote . Talks on these topics are solicited. Please send a title and short description to the session organizers by April 15, 1996, ie Today! Session Organizers: : h.rzepa@ic.ac.uk - Prof. Henry Rzepa smb@smb.chem.niu.edu Prof. Steven Bachrach THPierce@RohmHaas.Com - Dr. Tom Pierce Thank you for your time. ----- Sincerely, Tom Pierce - THPierce@RohmHaas.Com - Computational Chemist "These opinions are those of the writer and not the Rohm and Haas Company." -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: owner-chemistry@ccl.net -- Original Sender From: Address: THPierce@rohmhaas.com CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search Web: http://www.ccl.net/chemistry.html