From chemistry-request@server.ccl.net Thu Apr 17 03:39:27 2003 Received: from col-msxproto2.col.missouri.edu ([128.206.3.152]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3H7dR313593 for ; Thu, 17 Apr 2003 03:39:27 -0400 Received: from COL-EMAIL2 ([128.206.3.132]) by col-msxproto2.col.missouri.edu with Microsoft SMTPSVC(5.0.2195.6673); Thu, 17 Apr 2003 02:39:26 -0500 X-MimeOLE: Produced By Microsoft Exchange V6.0.6375.0 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="UTF-8" Subject: About simulated annealing by charmm Date: Thu, 17 Apr 2003 02:39:26 -0500 Message-ID: <3393392D7484804AAC174AA1D24F08551DF380@COL-EMAIL2.col.missouri.edu> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: About simulated annealing by charmm Thread-Index: AcMEtHjtbYl35+0URiqX9OBJ1240CA== From: "Hu, Xiaohua" To: X-OriginalArrivalTime: 17 Apr 2003 07:39:26.0928 (UTC) FILETIME=[79202500:01C304B4] Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id h3H7dR313594 Hi all, I read a paper in which the simulated annealing was carried out by CHARMM. I am a newbie of CHARMM. Could anybody tell me where I can find a sample script or general idea about this procedure (except CHARMM manual) so that I am able to learn it. Thank you so much! Best Shawn Chemistry Department Univeristy of Missouri-Columbia From chemistry-request@server.ccl.net Wed Apr 16 22:04:59 2003 Received: from pacific-carrier-annex.mit.edu ([18.7.21.83]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3H24x306589 for ; Wed, 16 Apr 2003 22:04:59 -0400 Received: from grand-central-station.mit.edu (GRAND-CENTRAL-STATION.MIT.EDU [18.7.21.82]) by pacific-carrier-annex.mit.edu (8.12.4/8.9.2) with ESMTP id h3H24xGt002704 for ; Wed, 16 Apr 2003 22:04:59 -0400 (EDT) Received: from melbourne-city-street.mit.edu (MELBOURNE-CITY-STREET.MIT.EDU [18.7.21.86]) by grand-central-station.mit.edu (8.12.4/8.9.2) with ESMTP id h3H24xTI004509 for ; Wed, 16 Apr 2003 22:04:59 -0400 (EDT) Received: from mit.edu (EASTGATE-NINETY-ONE.MIT.EDU [18.97.5.91]) ) by melbourne-city-street.mit.edu (8.12.4/8.12.4) with ESMTP id h3H24xU8021709 for ; Wed, 16 Apr 2003 22:04:59 -0400 (EDT) Message-ID: <3E9E0BC8.80003@mit.edu> Date: Wed, 16 Apr 2003 22:04:56 -0400 From: Daeyeon Lee User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.2) Gecko/20030208 Netscape/7.02 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Need Help on Simulation of Polymer Blend/copolymer system Content-Type: multipart/alternative; boundary="------------030606030008040405000601" --------------030606030008040405000601 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Hello all, I am a graduate student in the Chem Eng Dept at MIT taking a course on the statistical mechanics of polymers. We have a final project that we must submit by the end of the term (May 8th) and my project is to investigate the compatibilizing effect of block copolymers in immiscible polymer blend system. Specifically, it will be a blend of A and B homopolymer with A-C diblcok copolymer as a compatibilizer. Unfortunately, I have no experience with computational simulations and am stuck from the beginning. I have read some papers where people have used Monte Carlo simulations. I hope there is a software package that I can use to do simple simulations to study this kind of system. I have used Biosym several times and I know that there is an amorphous cell module which may work for me but I am still not sure if this is where I should start. I would sincerely appreciate it if someone with some experience in this kind of work could help me out or offer some advice. Thank you very much. Sincerely, Daeyeon Lee -- Daeyeon Lee Department of Chemical Engineering/PPST Massachusetts Institute of Technology Room 66-353 77 Massachusetts Ave. Cambridge, MA 02139 Tel: (617) 253-6477 E-mail: daeyeon@mit.edu --------------030606030008040405000601 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Hello all,

I am a graduate student in the Chem Eng Dept at MIT taking a course on the statistical mechanics of polymers.  We have a final project that we must submit by the end of the term (May 8th) and my project is to investigate the compatibilizing effect of block copolymers in immiscible polymer blend system.  Specifically, it will be a blend of A and B homopolymer with A-C diblcok copolymer as a compatibilizer.  Unfortunately, I have no experience with computational simulations and am stuck from the beginning. I have read some papers where people have used Monte Carlo simulations.  I hope there is a software package that I can use to do simple simulations to study this kind of system.  I have used Biosym several times and I know that there is an amorphous cell module which may work for me but I am still not sure if this is where I should start.  I would sincerely appreciate it if someone with some experience in this kind of work could help me out or offer some advice. Thank you very much.

Sincerely,

Daeyeon Lee


--
daeyeon signature
Daeyeon Lee
Department of Chemical Engineering/PPST
Massachusetts Institute of Technology 
Room 66-353
77 Massachusetts Ave.
Cambridge, MA 02139

Tel:  (617) 253-6477
E-mail: daeyeon@mit.edu

--------------030606030008040405000601-- From chemistry-request@server.ccl.net Wed Apr 16 22:51:47 2003 Received: from mail.shcnc.ac.cn ([202.127.16.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3H2ph307632; Wed, 16 Apr 2003 22:51:46 -0400 Received: from pc29 ([202.127.19.62]) by mail.shcnc.ac.cn (8.12.1/8.12.1) with SMTP id h3HIs3a5000078; Thu, 17 Apr 2003 11:54:03 -0700 (PDT) Message-Id: <200304171854.h3HIs3a5000078@mail.shcnc.ac.cn> Date: Thu, 17 Apr 2003 10:52:44 +0800 From: Jinzhi Tan Reply-To: jztan@mail.shcnc.ac.cn To: "chemistry-request@server.ccl.net" CC: "chemistry@ccl.net" Subject: how to deal with box in CHARMM? Organization: SIMM-DDDC X-mailer: FoxMail 4.0 beta 2 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id h3H2pl307633 Dear Sir: I generate a large box containing 15000 waters. When I try to put the protein into the box, it always occur "string too small" error and stop. Maybe the number of water are too many. I don't know how to split the box into several segments? or split the box into small box? Thank you very much! Best wishes, Jinzhi Tan 2003-4-17 ************************************* Jinzhi Tan Ph.D. student Chinese Academy of Sciences Shanghai 200031, China Phone :086-21-64311833-507 Fax :086-21-64318401 E-mail:jztan@mail.shcnc.ac.cn tanjinzhi@hotmail.com ************************************* From chemistry-request@server.ccl.net Thu Apr 17 11:33:39 2003 Received: from kafka.net.nih.gov ([165.112.130.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3HFXd307472 for ; Thu, 17 Apr 2003 11:33:39 -0400 Received: from pollux.cber.nih.gov (pollux.cber.nih.gov [128.231.52.5]) by kafka.net.nih.gov (8.12.9/8.12.9) with ESMTP id h3HFXcAd018914; Thu, 17 Apr 2003 11:33:38 -0400 (EDT) Date: Thu, 17 Apr 2003 11:11:21 -0400 From: Rick Venable To: Jinzhi Tan cc: "chemistry@ccl.net" Subject: Re: CCL:how to deal with box in CHARMM? In-Reply-To: <200304171854.h3HIs3a5000078@mail.shcnc.ac.cn> Message-ID: References: <200304171854.h3HIs3a5000078@mail.shcnc.ac.cn> ReplyTo: Rick_Venable@nih.gov MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 17 Apr 2003, Jinzhi Tan wrote: > Dear Sir: > I generate a large box containing 15000 waters. When I try to put the > protein into the box, it always occur "string too small" error and > stop. Maybe the number of water are too many. I don't know how to > split the box into several segments? or split the box into small box? > Thank you very much! At present, a CHARMM segment cannot contain more than 9999 residues; you *must* split your water into at least 2 segments. You will also probably need to use a CHARMM version compiled with LARGE or XXLARGE size specification for a system with this many atoms. Note that a fairly new developmental version of CHARMM undergoing preliminary tests now allows for (10**8 - 1) residues per segment. =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable@nih.gov ALT email: rvenable@speakeasy.org ------------------------------------- "Don't blame me, I voted for Kang." Homer =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= From chemistry-request@server.ccl.net Thu Apr 17 10:03:47 2003 Received: from iris.chimfarm.unipg.it ([141.250.13.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3HE3l304859 for ; Thu, 17 Apr 2003 10:03:47 -0400 Received: from nettuno.chimfarm.unipg.it ([141.250.13.84] ident=1000) by iris.chimfarm.unipg.it with esmtp (Exim 2.04 #2) id 196IQ2-0001L9-00 for chemistry@ccl.net; Thu, 17 Apr 2003 16:03:51 -0700 Date: Thu, 17 Apr 2003 16:00:22 +0000 (UTC) From: Mirco Meniconi X-X-Sender: mirco@nettuno.chimfarm.unipg.it To: chemistry@ccl.net Subject: MM3 model for water Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, I'm tryng to calculate the interaction energy beetwen a water molecule and a very large molecule, in each point of SAS, with MM3 force field. In order to minimize calculation time I need to treat the water molecule as a single atom. Does anybody knowm some water parametrization that I can use with MM3 FF? thank'you -- Mirco Meniconi PhD candidate dip. chimica e tecnologia del farmaco via del liceo 1 06100 Perugia university of Perugia (ITALY) phone: +39 075 585 5169 phone: +39 075 585 5114 e-mail: mirco.me@inwind.it e-mail: mirco@unipg.it Prima ti ignorano. Poi ridono di te. Poi ti combattono. Poi tu vinci. From chemistry-request@server.ccl.net Thu Apr 17 15:24:18 2003 Received: from mrelay2.inscc.utah.edu ([155.101.3.58]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3HJOIE01304 for ; Thu, 17 Apr 2003 15:24:18 -0400 Received: from mail.inscc.utah.edu (mail.inscc.utah.edu [155.101.3.59]) by mrelay2.inscc.utah.edu (Postfix) with ESMTP id 688071CE53 for ; Thu, 17 Apr 2003 16:23:34 -0400 (EDT) Received: from mercury.hec.utah.edu (tntpc2.hec.utah.edu [155.101.19.38]) by mail.inscc.utah.edu with ESMTP id OAA07148 for ; Thu, 17 Apr 2003 14:23:34 -0600 (MDT) Message-ID: <3E9F0D45.1ED358C4@mercury.hec.utah.edu> Date: Thu, 17 Apr 2003 14:23:33 -0600 From: Atchara Wijitkosoom X-Mailer: Mozilla 4.79 [en] (Windows NT 5.0; U) X-Accept-Language: en MIME-Version: 1.0 To: "Chemsitry CCL.NET" Subject: B-factor Content-Type: multipart/alternative; boundary="------------15B731B5D4A9DFE11D80098A" --------------15B731B5D4A9DFE11D80098A Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit To whom it may concern, Does anybody know how to get the B-factor per residue from X-ray structure? Thank you very much in advance. Yours, Atchara --------------15B731B5D4A9DFE11D80098A Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit To whom it may concern,
 
Does anybody know how to get the B-factor per residue > from X-ray structure? Thank you very much in advance.

Yours,
Atchara --------------15B731B5D4A9DFE11D80098A--