From chemistry-request@ccl.net Thu Oct 9 04:27:14 2003 Received: from mail.fescomail.net ([202.94.7.253]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h998Qedm027509 for ; Thu, 9 Oct 2003 04:26:42 -0400 Received: (qmail 68240 invoked by uid 2000); 9 Oct 2003 16:27:06 -0000 Message-ID: <20031009162706.68239.qmail:at:mail.fescomail.net> From: "xiongying99" To: chemistry:at:ccl.net Subject: CCL:the parameter for Zn in autodock? Date: Thu, 09 Oct 2003 16:27:06 +0000 Mime-Version: 1.0 Content-Type: text/plain; format=flowed; charset="gb2312" Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=3.3 required=7.0 tests=DEAR_SOMETHING,FROM_ENDS_IN_NUMS version=2.55 X-Spam-Level: *** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear sir, Now I use ADT( autodocktools)to dock a ligand to an enzyme, when I run grid command, I met the following information :" the protein has unusual type:Z". I must type the values of Rij and epsij. Does Z mean atom Zn? What parameter should I type for it? Thank you! ---------------------------------------------------------------- FESCOmail.net From chemistry-request@ccl.net Thu Oct 9 00:24:13 2003 Received: from mail.chem.tamu.edu (mail.chem.tamu.edu [165.91.176.8]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h994Ngdm022251 for ; Thu, 9 Oct 2003 00:23:42 -0400 Received: from [165.91.178.2] (HELO yubopclab) by mail.chem.tamu.edu (CommuniGate Pro SMTP 4.1.3) with SMTP id 214924; Wed, 08 Oct 2003 23:23:42 -0500 Message-ID: <001801c38e1d$1b22d810$02b25ba5@yubopclab> From: "Yubo Fan" To: Subject: Small imaginary frequency and grid Date: Wed, 8 Oct 2003 23:23:35 -0500 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0015_01C38DF3.32221690" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1158 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-Spam-Status: No, hits=4.5 required=7.0 tests=HTML_30_40,HTML_MESSAGE,RCVD_IN_OSIRUSOFT_COM, X_OSIRU_OPEN_RELAY version=2.55 X-Spam-Level: **** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) This is a multi-part message in MIME format. ------=_NextPart_000_0015_01C38DF3.32221690 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi, everyone, Sometimes, some imaginary frequencies with very small absolute value are = very difficult to get rid of when I run frequency calculations on G98. = Those vibrational modes are the rotations of phosphines by the TM-P = bond. If I increase the grid for the integral, these imaginary = frequencies disappears. So, two problems arise. 1) Can this phenomenon be proved mathematically? 2) How can I get the correct thermochemistry results if I don't want to = increase the grid for all structures? Thanks in advance, Yubo =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Dr. Yubo Fan Email: yubofan:at:mail.chem.tamu.edu Department of Chemistry Tel: 1-979-845-7222 Texas A&M University College Station, TX 77843 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D ------=_NextPart_000_0015_01C38DF3.32221690 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Hi, everyone,

Sometimes, some imaginary frequencies = with very=20 small absolute value are very difficult to get rid of when I run = frequency=20 calculations on G98. Those vibrational modes are the rotations of = phosphines by=20 the TM-P bond. If I increase the grid for the integral, these = imaginary=20 frequencies disappears. So, two problems arise.

1) Can this phenomenon be proved=20 mathematically?

2) How can I get the correct = thermochemistry=20 results if I don't want to increase the grid for all = structures?

Thanks in advance,

Yubo

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Dr. Yubo=20 Fan &nbs= p; =20 Email: yubofan:at:mail.chem.tamu.edu=
Department=20 of Chemistry Tel: 1-979-845-7222
Texas = A&M=20 University
College Station, TX=20 77843
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D

------=_NextPart_000_0015_01C38DF3.32221690-- From chemistry-request@ccl.net Thu Oct 9 03:09:46 2003 Received: from ozone.cs.vu.nl (ozone.cs.vu.nl [130.37.24.158]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9979Ddm025480 for ; Thu, 9 Oct 2003 03:09:14 -0400 Received: from chem.vu.nl (far27.chem.vu.nl [130.37.148.106]) by ozone.cs.vu.nl with esmtp (Smail #87) id m1A7Uv5-000NGqC; Thu, 9 Oct 2003 09:09 +0200 Message-ID: <3F818D0F.2080709:at:chem.vu.nl> Date: Mon, 06 Oct 2003 17:41:03 +0200 From: Anton Feenstra User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:1.3.1) Gecko/20030425 X-Accept-Language: en-us, en MIME-Version: 1.0 To: Ru-Zhen Li CC: chemistry:at:ccl.net Subject: CCL:anyone knows WHAT IF check on protein well? References: <019b01c38b51$88e644f0$432b258a@lucylaptop> In-Reply-To: <019b01c38b51$88e644f0$432b258a@lucylaptop> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.9 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT, RCVD_IN_OSIRUSOFT_COM,REFERENCES,REPLY_WITH_QUOTES, USER_AGENT_MOZILLA_UA,X_ACCEPT_LANG,X_OSIRU_OPEN_RELAY version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Ru-Zhen Li wrote: > Dear all, > > Now I am doing a WHAT IF check of 1n5u, and I got some results, i think > if I want to do some simulation work on the protein, I should make sure > that every serious warning or error on the check report is fixed, but how? In my experience, I can normally take a file from the pdb, minimize it, add water, equilibrate with position restraints on the protein and start an MD simulation on it right away. I never perform a WhatCheck or ProCheck before doing this. IMHO, if the MD runs, the structure is OK. (By the way, I'm using Gromacs for the minimization, equilibration and MD.) -- Groetjes, Anton _____________ _______________________________________________________ | | | | _ _ ___,| K. Anton Feenstra | | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam | |( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands | | \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 | | | Feenstra:at:chem.vu.nl - www.chem.vu.nl/~feenstra/ | | | "If You See Me Getting High, Knock Me Down" | | | (Red Hot Chili Peppers) | |_____________|_______________________________________________________| From chemistry-request@ccl.net Thu Oct 9 05:37:04 2003 Received: from dct7243.dct.tudelft.nl (dct7243.dct.tudelft.nl [130.161.197.243]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h999aVdm029407 for ; Thu, 9 Oct 2003 05:36:32 -0400 Received: (from jacek@localhost) by dct7243.dct.tudelft.nl (8.11.6/8.11.6) id h999ZNQ30331 for chemistry_at_ccl.net; Thu, 9 Oct 2003 11:35:23 +0200 Date: Thu, 9 Oct 2003 11:35:23 +0200 From: Jacek Wojdel To: chemistry_at_ccl.net Subject: CCL: Vanderbilt uspps transferability Message-ID: <20031009113523.A30165_at_dct7243.dct.tudelft.nl> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.2.5.1i X-Spam-Status: No, hits=-2.5 required=7.0 tests=USER_AGENT_MUTT version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear CCLers, I recently stumbled on a problem when using uspps for transition metal complexes: the uspps do not seem to be transferable between configurations that differ in the spin state. Is anyone aware of some literature concerning transferability of uspps for hi/lo-spin states (like in weak/strong ligand field), or on influence of pseudization method (number of beta-functions etc) on recapturing the proper spin state of the complex? Any pointers even remotely related would be appreciated. Regards, Jacek Wojdel -- +-------------------------------------+ |from: J.C.Wojdel | | J.C.Wojdel_at_tnw.tudelft.nl | +-------------------------------------+ From chemistry-request@ccl.net Thu Oct 9 21:45:57 2003 Received: from gip2.u-picardie.fr (gip2.u-picardie.fr [193.49.184.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9A1jPdm017307 for ; Thu, 9 Oct 2003 21:45:26 -0400 Received: by gip2.u-picardie.fr (Postfix, from userid 33) id 313BC9A5C; Fri, 10 Oct 2003 03:45:25 +0200 (CEST) To: gamess-l(at)gl.ciw.edu, chemistry(at)ccl.net Subject: Optimization accuracy in GAMESS-US Message-ID: <1065750325.3f860f351c95c(at)webmail.u-picardie.fr> Date: Fri, 10 Oct 2003 03:45:25 +0200 (CEST) From: FyD MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: IMP/PHP IMAP webmail program 2.2.6 X-Spam-Status: No, hits=0.0 required=7.0 tests=USER_AGENT version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear All, I am interested in minimizing structures using smaller OPTTOL threshold than the default one in GAMESS-US. I decided to decrease also QMTTOL=1.0E-7, ICUT=21 and ITOL=10 to increase the accuracy. Is there some other parameters that would also affect the optimization accuracy ? For instance, if I look at the minimization ouput, in the "integral transformation" options, there a cutoff = 1.0E-09 by default. Surprisingly, it is only defined in the GAMESS documentation for MP2 calculations... As I do HF minimization, I wonder if it is possible/interesting to decrease this cutoff ? Thanks, regards, Francois From chemistry-request@ccl.net Thu Oct 9 12:43:26 2003 Received: from web21010.mail.yahoo.com (web21010.mail.yahoo.com [216.136.227.64]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h99Ggtdm006583 for ; Thu, 9 Oct 2003 12:42:55 -0400 Message-ID: <20031009164254.74832.qmail[at]web21010.mail.yahoo.com> Received: from [148.218.36.120] by web21010.mail.yahoo.com via HTTP; Thu, 09 Oct 2003 09:42:54 PDT Date: Thu, 9 Oct 2003 09:42:54 -0700 (PDT) From: Cesar Millan Subject: CCL: Total solvation energy on DELPHI To: CHEMISTRY[at]ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Spam-Status: No, hits=0.0 required=7.0 tests=FROM_HAS_UNDERLINE_NUMS version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi everyone: I'm trying to calculate the total solvation energy of a molecule using DELPHI program, but I'm a little confused about the definition of reaction field and solvation energy? Are these terms the same thing? Or you have to calculate the nonpolar solvation energy with other program? and How these terms change if I use a ionic strength distint of zero? Any help would be appreciated. Cesar Millan Pacheco Ph. D. Student Universidad Autonoma del Estado de Morelos. __________________________________ Do you Yahoo!? The New Yahoo! Shopping - with improved product search http://shopping.yahoo.com From chemistry-request@ccl.net Thu Oct 9 15:02:45 2003 Received: from mail.uh.edu (SanJacinto.Mail.UH.EDU [129.7.235.116]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h99J2Ddm009984 for ; Thu, 9 Oct 2003 15:02:13 -0400 Received: from conversion-daemon by mail.uh.edu (Sun Internet Mail Server sims.4.0.2001.07.26.11.50.p9) id <0HMI008017JBCX[at]mail.uh.edu> for chemistry[at]ccl.net; Thu, 9 Oct 2003 14:02:05 -0500 (CDT) Received: from localhost (Colorado.Mail.UH.EDU [129.7.235.114]) by mail.uh.edu (Sun Internet Mail Server sims.4.0.2001.07.26.11.50.p9) with ESMTP id <0HMI008637J42Z[at]mail.uh.edu> for chemistry[at]ccl.net; Thu, 09 Oct 2003 14:01:52 -0500 (CDT) Date: Thu, 09 Oct 2003 14:01:52 -0500 (CDT) From: Niharendu.Choudhury[at]mail.uh.edu Subject: How to calculate PMF between two solute molecule in a MD simulation. To: chemistry[at]ccl.net Message-id: <482550261.1065726112806.JavaMail.root@localhost> MIME-version: 1.0 X-Mailer: Sun(TM) Web Access 1.2 Content-type: text/plain; charset=ISO-8859-1 Content-transfer-encoding: 7BIT X-Spam-Status: No, hits=0.8 required=7.0 tests=NO_REAL_NAME version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear CCLers, I have a system of two solute atoms in a solvent and I am running MD for various fixed distances (r_0) between two solute atoms. Can anybody tell me in details how to calculate the PMF between these two solute molecules using say Free endrgy Perturbation method. Is there any code available which can be directly added to my MD code. It will be helpful if anybody let me know any literature which describes these methods in details. Thanks in advance Niharendu Choudhury From chemistry-request@ccl.net Thu Oct 9 16:28:33 2003 Received: from samuel.unet.maine.edu (samuel.unet.maine.edu [130.111.39.86]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h99KS2dm011712 for ; Thu, 9 Oct 2003 16:28:02 -0400 Received: from osgood.unet.maine.edu (osgood.unet.maine.edu [130.111.39.64]) by samuel.unet.maine.edu (8.12.8/8.12.8) with ESMTP id h99KNulP025461 for ; Thu, 9 Oct 2003 16:23:57 -0400 Received: from adamantane.maine.edu (Adamantane.umecit.maine.edu [130.111.234.157]) by osgood.unet.maine.edu (8.11.6/8.11.6) with ESMTP id h99KOKP19224 for ; Thu, 9 Oct 2003 16:24:20 -0400 Message-Id: <5.1.1.6.0.20031009162232.00a21ec0[at]mail.maine.edu> X-Sender: rcfort[at]mail.maine.edu X-Mailer: QUALCOMM Windows Eudora Version 5.1.1 Date: Thu, 09 Oct 2003 16:24:59 -0400 To: chemistry[at]ccl.net From: "Raymond C. Fort Jr." Subject: Grace Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed X-MailScanner: Found to be clean, Found to be clean X-MailScanner-Information: Please contact the ISP for more information X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Apologies for being a bit off topic again! Does anyone have the source for an earlier version of grace (xmgrace) that will compile under Red Hat 7.2 ? I'm not eager to upgrade my Linux in the middle of teaching a course on the machines, but we really could use grace (or xmgr) for that matter. Thanks in advance for any help! Professor Ray Fort Jr. Voice: (207)-581-1180 Department of Chemistry FAX: (207)-581-1191 University of Maine EMail: rcfort[at]maine.edu Orono, ME 04469 Web: chemistry.umeche.maine.edu/fort.html Molecular modeling of organic and biological molecules; chemistry of lignin and cellulose