From chemistry-request@server.ccl.net Sat May 12 17:22:28 2001 Received: from www.ndsu.nodak.edu ([134.129.111.121]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4CLMRI27281 for ; Sat, 12 May 2001 17:22:27 -0400 Received: (from nobody@localhost) by www.ndsu.nodak.edu (8.10.1/8.10.1) id f4CLMQe16093; Sat, 12 May 2001 16:22:26 -0500 Date: Sat, 12 May 2001 16:22:26 -0500 Message-Id: <200105122122.f4CLMQe16093@www.ndsu.nodak.edu> X-Authentication-Warning: www.ndsu.nodak.edu: nobody set sender to xin_hu@ndsu.nodak.edu using -f From: xin_hu@ndsu.nodak.edu To: Benjamin J Gross Reply-To: xin_hu@ndsu.nodak.edu Cc: chemistry@ccl.net References: <3AFC8745.4D91@smtpserver2.Princeton.EDU> In-Reply-To: <3AFC8745.4D91@smtpserver2.Princeton.EDU> MIME-Version: 1.0 Content-Type: text/plain Content-Transfer-Encoding: 8bit User-Agent: IMP/PHP3 Imap webMail Program 2.0.11 Sender: xin_hu@ndsu.nodak.edu Subject: Re: CCL:installing autodock tools Hi, I got the same problem before. Try to add the path of Pmv to the .bash_profile. It may work. I did as following: PATH=$PATH: /home/she lver/Program/python1.5/i86Linux2/bin:/home/shelver/Program/python1.5/share/lib/p ython1.5/site-packages/AutoDockTools:/home/shelver/Program/python1.5/share/lib/p ython1.5/site-packages/Pmv Unfornately I still have installed the ADT program properly. The problem is about the OpenGL. I was told to install the openGL1.5, but I do not know where to download the openGL1.5 for Linux. If you know or someone else know that, please let me know. The following is the error I got while i try to run pmv or adt: Run PMV from /home/shelver/Program/python1.5/share/lib/python1.5/site-packages/Pmv Traceback (innermost last): File "/home/shelver/Program/python1.5/share/lib/python1.5/site-packages/Pmv/pmv", line 53, in ? from Pmv.moleculeViewer import MoleculeViewer File "/home/shelver/Program/python1.5/share/lib/python1.5/site-packages/Pmv/moleculeViewer.py", line 15, in ? from MolKit.protein import Protein File "/home/shelver/Program/python1.5/share/lib/python1.5/site-packages/MolKit/protein.py", line 401, in ? from Pmv.extruder import Rectangle2D, Sheet2D, Extrude, Rectangle2DDup, Circle2D File "/home/shelver/Program/python1.5/share/lib/python1.5/site-packages/Pmv/extruder.py", line 16, in ? from OpenGL import GL File "/home/shelver/Program/python1.5/share/lib/python1.5/site-packages/OpenGL/GL/__init__.py", line 4, in ? from _opengl_num import * ImportError: /home/shelver/Program/python1.5/share/lib/python1.5/site-packages/OpenGL/shared/linux2/_opengl_nummodule.so: undefined symbol: glPolygonOffsetEXT hit enter to continue hopefully someone give me a help. xin dept of pharmacy NDSU Fargo, ND 58102 Quoting Benjamin J Gross : > Hi everyone, > Sorry if my question is trivial: I'm a linux/python/autodock newbie. I'm > having some trouble getting autodock tools or Pmv to work. When I try to > run the pmv script I get the following error: > > [bgross@bgross Pmv]$ pmv > Traceback (innermost last): > File "/home/bgross/tools/share/lib/python1.5/site-packages/Pmv/pmv", line > 49, in ? > import Pmv > ImportError: No module named Pmv > > Has anyone solved anything similar? > > Thanks in advance. > > Ben > > > > > -= 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 Sun May 13 08:59:22 2001 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4DCxMI13431 for ; Sun, 13 May 2001 08:59:22 -0400 Received: from sscu.iisc.ernet.in (IDENT:root@sscu.iisc.ernet.in [144.16.75.2]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id IAA12373 for ; Sun, 13 May 2001 08:59:18 -0400 (EDT) Received: from localhost (munshi@localhost) by sscu.iisc.ernet.in (8.9.3/8.9.3) with ESMTP id SAA28176 for ; Sun, 13 May 2001 18:42:45 +0530 Date: Sun, 13 May 2001 18:42:45 +0530 (IST) From: "Mr. Parthapratim Munshi" To: chemistry@ccl.net Subject: Suggestion pl. Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, I am from India, Indian Institute of Science, Bangalore. Depertment Solid State & Structural Chemistry Unit, can you suggest me thet how to calculate the dipole moment of organic molecules? e.g. for coumarin(C9H6O2)......is there any pocedure for theoritical calculation? so far i know that if i know the bonding moment then i can calculate the total dipole momet of the system..........but from where can i get the information of bonding moment can u supply any table or chart from where i can get the information...............i'm waiting for the sharp reply ...... with regards Parthapratim Munshi From chemistry-request@server.ccl.net Sun May 13 10:06:35 2001 Received: from vytautas.vdu.lt ([193.219.38.33]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4DE6YI13775 for ; Sun, 13 May 2001 10:06:34 -0400 Received: from vaidila.vdu.lt ([193.219.38.52] ident=root) by vytautas.vdu.lt with esmtp for CHEMISTRY@ccl.net id 14ywW0-0006Yk-00; Sun, 13 May 2001 16:06:32 +0200 Received: from vaidila.vdu.lt (vejas.vdu.lt [193.219.38.82]) by vaidila.vdu.lt (8.9.3/8.9.3) with ESMTP id QAA12853 for ; Sun, 13 May 2001 16:13:05 +0200 (GMT) Message-ID: <3AFDEC00.A2E5DD99@vaidila.vdu.lt> Date: Sun, 13 May 2001 04:05:52 +0200 From: "art'" X-Mailer: Mozilla 4.7 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 CC: CHEMISTRY@ccl.net Subject: CCL: AutoDock - PDBQ charges ... References: <01010514402700.01598@koronium> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, CCL'ers, The user can shoose not to model non-polar hydrogens and they could be excluded > from ligand structure. The question: Should heavy atoms, with excluded non-polar hydrogen, retain thier original charges, OR the charges of excluded hydrogens should be sumed to that heavy atom charge, from they were excluded ? (here could be an example for the modeling alkil- recidues...) Best wishes to all A.Ziemys