From chemistry-request@server.ccl.net Fri Nov 15 05:43:29 2002 Received: from atc.atccu.chula.ac.th ([192.207.64.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAFAhND26430 for ; Fri, 15 Nov 2002 05:43:28 -0500 Received: from localhost (koonwadee@localhost) by atc.atccu.chula.ac.th (8.9.3/8.9.3) with ESMTP id RAA19568 for ; Fri, 15 Nov 2002 17:55:01 +0700 Date: Fri, 15 Nov 2002 17:55:01 +0700 (ICT) From: To: chemistry@ccl.net Subject: Dear All Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear All, I'm using AutoDock 2.4 and 3.0.5. I have some problems. I would appreciate if you could help. My questions are : 1. I performed the docking with conformational search and found the term " inter energy". How does the AutoDock 2.4 calculate the internal energy of small molecule? What's the form of potential functions that leads to such internal energy of small molecule? 2. I ran AutoDock 3.0.5 on Linux RedHat 7.2 but the program was terminated with error. The error message is " a, m, s out of order in mltmod -ABORT! a=784306273 s=0 m=2147483399 mltmod requires: 0; Fri, 15 Nov 2002 10:03:12 -0500 Received: from lrb.ap-hop-paris.fr (localhost [127.0.0.1]) by pasteur.ap-hop-paris.fr (iPlanet Messaging Server 5.1 (built May 7 2001)) with ESMTP id <0H5M00EKLHSYXS@pasteur.ap-hop-paris.fr> for chemistry@ccl.net; Fri, 15 Nov 2002 16:02:59 +0100 (MET) Date: Fri, 15 Nov 2002 14:52:48 -0800 From: Pong Subject: Need your help Sender: pong@ap-hop-paris.fr To: chemistry@ccl.net Message-id: <3DD57AC0.93AA0988@lrb.ap-hop-paris.fr> Organization: Service de Biochimie et de biologie moleculaire MIME-version: 1.0 X-Mailer: Mozilla 4.75C-SGI [en] (X11; I; IRIX 6.5 IP32) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT X-Accept-Language: en Dear memeber of CCL, I'm Mr PONG. I would like to have your advice about the program to calculate the geometry of chemical structure. I mean, to measure the distance, aggle and dihedral angle. Yes, there are many programs which is very easy to do that, I know. But I need the program to measure all compounds at the same time. This was due to I have thousands conformers generation by systematic search. All have the same atom type and number, just only different in conformers. Sure! they must be difference in term of geometry (distance, angle, and torsional angle). Is there any program? that I can specify the atom that I want to measure, for example A-B, A-B-C and A-B-C-D for distance, angle, and torsional angle, respectively. And use this atom point to be calculate for all conformers in the same time, not need to select one conformer and calculate for each one. It's not possible to do if i have many thoudsands conformers. So, if you have any program capable to to that, could you please to inform me too. I would like to thank for all your kindness to consider my problem. Thank you . Pong From chemistry-request@server.ccl.net Fri Nov 15 09:51:53 2002 Received: from phm.utoronto.ca ([128.100.70.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAFEprD03699 for ; Fri, 15 Nov 2002 09:51:53 -0500 Received: from MditDell (mditdell.mdit.utoronto.ca [128.100.251.12]) by phm.utoronto.ca (8.9.3+Sun/8.9.3) with SMTP id JAA16242 for ; Fri, 15 Nov 2002 09:51:50 -0500 (EST) From: "William Wei" To: "CCLers" Subject: Homology modeling software? Date: Fri, 15 Nov 2002 21:50:22 -0500 Message-ID: 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 IMO, Build 9.0.2416 (9.0.2910.0) X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Importance: Normal Hi all, Does anyone know about more functional Homology modeling software than Composer in sybyl package. What I want is I can interact more while I do the modeling, for example, I want a "gap" some where, it is very difficult to do that in Composer. Thank you for any information. Regards, William ------------------------- William Wei Faculty of Pharmacy 19 Russell Street Toronto, ON. M5S 2S2 Tel: 1-416-946-8469 Fax: 1-416-978-8511 Email: william@phm.utoronto.ca william.wei@utoronto.ca From chemistry-request@server.ccl.net Fri Nov 15 07:12:39 2002 Received: from nomina.net.lu.se ([130.235.132.90]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAFCCdD30144 for ; Fri, 15 Nov 2002 07:12:39 -0500 Received: from csxp (CS-XP1800.mig.lu.se [130.235.104.90]) by nomina.net.lu.se (8.9.3/8.9.0) with SMTP id NAA09763 for ; Fri, 15 Nov 2002 13:13:07 +0100 (MET) Message-ID: <000a01c28ca0$b2ffa6b0$5a68eb82@csxp> From: =?iso-8859-1?Q?Emanuel_Bj=F6rne?= To: Subject: Integer charges on amino acid in AutoDock Date: Fri, 15 Nov 2002 13:15:34 +0100 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0007_01C28CA9.149DE910" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2720.3000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 This is a multi-part message in MIME format. ------=_NextPart_000_0007_01C28CA9.149DE910 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi! =20 Why is it necessary that the charge on each amino acid and the total = charge on the protein have integer values in AutoDock 3.0?=20 When I prepare a docking run with AutoDock Tools I get a warning message = saying that I should correct the charges on some amino acids before = running AutoDock. =20 Thank you for your time! Emanuel ------=_NextPart_000_0007_01C28CA9.149DE910 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Hi!

 

Why is it necessary that the charge on = each amino=20 acid and the total charge on the protein have integer values in AutoDock = 3.0?=20

When I prepare a docking run with = AutoDock Tools I=20 get a warning message saying that I should correct the charges on some = amino=20 acids before running AutoDock.

 

Thank you for your = time!

 

Emanuel

------=_NextPart_000_0007_01C28CA9.149DE910-- From chemistry-request@server.ccl.net Fri Nov 15 10:58:05 2002 Received: from vnuserv.vnuhcm.edu.vn ([203.162.44.33]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAFFw2D05894 for ; Fri, 15 Nov 2002 10:58:04 -0500 Received: from Services.hcmuns.edu.vn (Services.hcmuns.edu.vn [172.29.16.4]) by vnuserv.vnuhcm.edu.vn (8.9.3/8.8.7) with SMTP id GAA16439; Sat, 16 Nov 2002 06:11:57 GMT Received: from Server.vnuhcm.edu.vn. by VNU-Gateway with ESMTP Ver (1.1Plus) for recipient addresses : Received: from chemdep.hcmuns.edu.vn (IDENT:root@chemdep.hcmuns.edu.vn [172.29.2.202]) by Services.hcmuns.edu.vn (8.11.6/8.11.2) with ESMTP id gAFFgR504443 for ; Fri, 15 Nov 2002 22:42:27 +0700 Received: from winlinux ([172.29.2.207]) by chemdep.hcmuns.edu.vn (8.9.3/8.9.3) with SMTP id WAA06992 for ; Fri, 15 Nov 2002 22:12:40 -0700 Message-ID: <004901c28cbf$d23f2130$cf021dac@winlinux> From: "Minh Tung" To: Subject: Linux complier Date: Fri, 15 Nov 2002 22:58:21 +0700 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 6.00.2800.1090 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1090 Dear All , I using Gaussian on RedHat Linux 7.3 but I'm have some problems I can't known it well . I run my jobs Gaussian on Pentium III computer and it run good . However , when i run it on Pentium 4 , it can't convergence in SCF cycle and died at link 505 with the same I run on P3 . I think it may be the libary of Gaussian use and I try to comply Gaussian's libary using ATLAS. But the problem still can't resolve. Does I need another BLAS (like Intel Fortran) and how to use it exactly ? Any solutions will wellcome Thank in advantage ! Tung , Vo Minh tung092@chemdep.hcmuns.edu.vn Natural Science University Ho Chi Minh city , Vietnam