From chemistry-request@server.ccl.net Sat Jul 14 08:33:54 2001 Received: from fep6.online.sh.cn ([202.96.209.79]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6ECXr532513 for ; Sat, 14 Jul 2001 08:33:53 -0400 Received: from cadd2 ([61.151.29.176]) by fep6.online.sh.cn (InterMail vM.4.01.03.00 201-229-121) with SMTP id <20010714123500.UGNW24731.fep6.online.sh.cn@cadd2>; Sat, 14 Jul 2001 20:35:00 +0800 Date: Sat, 14 Jul 2001 20:34:38 +0800 From: Song Yun-long To: "chemistry@ccl.net" CC: "dock@cgl.ucsf.edu" Subject: DOCK4.0.1 how to add ligand information into potential sites X-mailer: FoxMail 3.0 beta 2 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 7bit Message-Id: <20010714123500.UGNW24731.fep6.online.sh.cn@cadd2> Dear sir, I want to dock a large database of small molecules into the active site of my interested enzyme using DOCK4.0.1 developed by Kuntz group.As I have the complex structure of enzyme with ligand. I want to add the ligand information,such as their coordinates, into the sphgen result(*.sph file) In many manuscripts, I saw in the site preparation, the authors include the ligand site (as in many receptor-ligand complex crystals)as potential binding site. How can I solve this problem? Can you help me?Any suggestions? Best wihes to you! Yours sincerely, Song Yun-long,Ph.D ~~~~~~~~~~~~~~~~~~~~~~~~~~ Dept of med.chem School of pharmacy Second Mil Med Univ Guohe Road,325 Shanghai,200433 P.R.China E-mail:songyunlong@263.net Tel:86-21-25070248 ~~~~~~~~~~~~~~~~~~~~~~~~~~ From chemistry-request@server.ccl.net Sat Jul 14 10:30:39 2001 Received: from baton.phys.lsu.edu ([130.39.182.71]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6EEUd503092 for ; Sat, 14 Jul 2001 10:30:39 -0400 Received: (from vani@localhost) by baton.phys.lsu.edu (8.9.2/8.9.2) id JAA24986; Sat, 14 Jul 2001 09:27:20 -0500 (CDT) Date: Sat, 14 Jul 2001 09:27:19 -0500 (CDT) From: Vemparala Satyavani To: chemistry@ccl.net Subject: Buckingham potential for polymers Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII The Buckingham potential has the form Aexp(-rB)-c/r^6. isn't it true that with this potential, when particle come closer than a distance, there is actually a huge attractive well? what actually prevents the particels to come closer? The repulsion part(aexp(-rB)) cannot actually counteract the attractive part at small distances. Combined with Coulomb(the attractive part), iam having some pathological conditions in the system. And also what is the best way to get an initial configuration? now iam just placing the chains on some lattice in a bigger box( so that they are well seperated) and then performing Pivot Monte Carlo on them before i Actually do MD. Is there a better way to get initial state? I suspect the initial state may be a problem for me. and finally even if i start at such a state, where the chains are well seperated, when MD is performed, there is a huge probability that any of the nonbonded atoms might come closer, and iam having similar problems irrespective of the size of the box. what is the best way to avoid the huge attractive well in the potential? Thanks a lot Vani From chemistry-request@server.ccl.net Sat Jul 14 12:10:37 2001 Received: from unlserve.unl.edu ([129.93.1.130]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6EGAb505786 for ; Sat, 14 Jul 2001 12:10:37 -0400 Received: from localhost (jmazlo@localhost) by unlserve.unl.edu (8.9.1a/8.9.2) with SMTP id KAA12918 for ; Sat, 14 Jul 2001 10:53:09 -0500 Date: Sat, 14 Jul 2001 10:53:09 -0500 (CDT) From: Johanna Mazlo To: chemistry@ccl.net Subject: autodock -active site Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL group, Is there a way to specify the active site of the receptor in autodock? I see a similar question was posted previously but not the answer. I will post the answer. Thank you Johanna Mazlo University of Nebraska Lincoln, NE 68588-0304 From chemistry-request@server.ccl.net Sat Jul 14 11:36:33 2001 Received: from mta5.263.net ([202.96.44.47]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6EFaW505594 for ; Sat, 14 Jul 2001 11:36:32 -0400 Received: by mta5.263.net (Postfix, from userid 60001) id 36BDA1CA014D9; Sat, 14 Jul 2001 23:39:51 +0800 (CST) Message-Id: <3B5067C7.14728@mta5> Content-Type: Multipart/Alternative; boundary="Boundary-=_NRdOUemTGJiPMocXoOwCzlFtQrEi" Date: Sat, 14 Jul 2001 23:39:51 +0800 (CST) From: "刘鑫杰" To: chemistry@ccl.net Subject: Does anyone know how to compute by Dalton? X-Priority: 3 X-Originating-IP: [166.111.26.197] X-Mailer: COREMAIL --Boundary-=_NRdOUemTGJiPMocXoOwCzlFtQrEi Content-Type: Text/Plain Content-Transfer-Encoding: 8bit Dalton is a very excellent quantum computation software.I want to use it to compute some little molecule on exciting state.But I don't know how to do it.Does any one know the software and help me? My question is : Does anyone know how to do "COREHOLE" computing? How to fix up configuration when I have a HF computing? 欢迎使用263天下邮免费信箱 --Boundary-=_NRdOUemTGJiPMocXoOwCzlFtQrEi Content-Type: Text/HTML Content-Transfer-Encoding: 8bit Dalton is a very excellent quantum computation software.I want to use it to compute some little molecule on exciting state.But I don't know how to do it.Does any one know the software and help me?
My question is :
Does anyone know how to do "COREHOLE" computing?
How to fix up configuration when I have a HF computing?
欢迎使用263天下邮免费信箱







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