From owner-chemistry@ccl.net Thu Jul 10 02:01:00 2008 From: "vijayan_rs_+_iicb.res.in" To: CCL Subject: CCL: Conjugate gradient error in Gromacs Message-Id: <-37320-080709085659-28682-AIwzPg531ro+fQfej27yzA=-=server.ccl.net> X-Original-From: vijayan_rs a iicb.res.in Content-Type: multipart/mixed; boundary="----=neXtPaRt_1215608471" Date: Wed, 9 Jul 2008 17:21:38 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: vijayan_rs/./iicb.res.in ------=neXtPaRt_1215608471 Content-Type: text/plain;charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear CCL subscribers, When i run a CG minimization for my protein i get an error message which states that "ERROR: can not do Conjugate Gradients with constraints (86562)' even though i have defined constraints = none in my MDP file, i presume that this could be due to the position constarint defined in my Topology file #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif so cany anybody tell me is this defined position restraint the source of error or is it due to the default LINCS constarin algroithim. Thanking in advance With Regards R.Vijayan R.Suyambu Kesava Vijayan Senior Research Fellow Structural Biology & Bioinformatics Division Indian Institute of Chemical Biology 4 Raja S.C. Mullick Road Jadavapur, Kolkata India -700 032 Phone: +91 33 2473 0492 Extn: 236 Mobile: +91 9831843540 Fax: +91 33 2473 5197, +91 33 2472 3967 ------=neXtPaRt_1215608471 Content-Type: text/plain; virus checked ------=neXtPaRt_1215608471-- From owner-chemistry@ccl.net Thu Jul 10 13:18:01 2008 From: "Thomas E Exner thomas.exner+/-uni-konstanz.de" To: CCL Subject: CCL: Protein-Ligand-Docking Software PLANTS Message-Id: <-37321-080710102025-15838-E/2kdxRdWHyZwKi/UaeVRg_._server.ccl.net> X-Original-From: "Thomas E Exner" Date: Thu, 10 Jul 2008 10:20:21 -0400 Sent to CCL by: "Thomas E Exner" [thomas.exner^_^uni-konstanz.de] Dear CCLers, we would like to announce our new protein-ligand docking software PLANTS (Protein-Ligand ANT System). The docking algorithm is based on a class of stochastic optimization algorithms called ant colony optimization (ACO). ACO is inspired by the behavior of real ants finding a shortest path between their nest and a food source. The following features are available: * ACO-based search engine * full ligand flexibility * two scoring functions (PLANTSCHEMPLP and PLANTSPLP) * flexible protein side-chains * rigid-body docking of multiconformer libraries into rigid and flexible receptors * constraint system * docking with selected explicit, displaceable water molecules * fully automatic ligand setup (rotatable bond identification, atom typing ...) * virtual screening * rescoring capability A trial version can be downloaded from http://www.tcd.uni-konstanz.de/research/plants.php. A free unrestricted license for non-profit organizations will be sent out on request. For commercial use, please contact the authors. Please, feel free to test it and sent us your comments. Thomas Exner University of Konstanz From owner-chemistry@ccl.net Thu Jul 10 15:06:00 2008 From: "Elaine Meng meng|*|cgl.ucsf.edu" To: CCL Subject: CCL: new Chimera release Message-Id: <-37322-080710142942-13352-fV4JUKrGJyGtA7pwN0TLVw(!)server.ccl.net> X-Original-From: "Elaine Meng" Date: Thu, 10 Jul 2008 14:29:38 -0400 Sent to CCL by: "Elaine Meng" [meng++cgl.ucsf.edu] Hi everybody, A new production release of UCSF Chimera is now available from: http://www.cgl.ucsf.edu/chimera/download.html#production Download is free for noncommercial use. Many improvements and new features have been added since the previous production release (Nov 2007), as detailed in the release notes: http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.2540.html For the time-challenged, here are just a few of the reasons you may want to use the new version: 1) new fetch types: - comparative models from ModBase - protein pocket data from CASTp database - small molecule structures from Pub3D - small molecule structures built from SMILES strings 2) surface improvements: - increased reliability - surface areas automatically calculated - Actions menu, other tools work on more types of surfaces 3) appearance: - default lighting changed to improve POV-Ray results - larger default scale - helix ribbon insides can be colored separately - 2D labels can include Greek letters and other symbols 4) new tools: Axes, EnsembleCluster, Solvate, Structure Diagram 5) new commands: export, mclip, molmap, perframe, ribinsidecolor, shape, solvate, topography, vop See the release notes for details. The production release includes versions for Windows, Mac/X11, Linux, SGI IRIX, and HP Tru64. The Mac Aqua version has been improved significantly, but for now remains a snapshot download: http://www.cgl.ucsf.edu/chimera/download.html#snapshots Enjoy! On behalf of the Chimera team, ----- Elaine C. Meng, Ph.D. meng*cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco From owner-chemistry@ccl.net Thu Jul 10 18:08:00 2008 From: "Richard Wood rwoodphd:+:msn.com" To: CCL Subject: CCL: Protein-Ligand CONSTRAINED Docking Message-Id: <-37323-080710180635-21210-N35B8OrhimRn0HSdvZG5fw[a]server.ccl.net> X-Original-From: "Richard Wood" Date: Thu, 10 Jul 2008 18:06:31 -0400 Sent to CCL by: "Richard Wood" [rwoodphd##msn.com] Hi all, I have a series of ligands which I've docked to a protein using Surflex-Dock as implemented in Sybyl. Unfortunately, my results don't explain some experimental observations so I would like to do some contrained docking. I've been looking into FlexX-Pharm, but it seems to only allow one to constrain an ELEMENT of the ligand to be a certain radius from a certain atom (which one can choose) in the protein target. For example, one can pick a nitrogen in a ligand to be within a 3.0 Angstrom radius of a given protein atom, say. This is problematic if your ligand has several nitrogens or carbons in them, as one cannot pick atom types or atom numbers. I'm wondering if there is a workaround to this; I'd like to stay with Sybyl as my boss wants me to use it, and we've decided Glide is not up to our standards. To conclude, I would like to be able to pick a particular ligand atom and constrain it to be a certain distance from a protein atom, that I again pick, and then dock it. As it stands now, I can only constrain a (any) nitrogen in my ligand (I think the fact that my ligand is not introduced at any point, prior to docking, into this process is what is problematic) to be within a radius of a protein atom, and not a fixed distance. Basically, I want to constrain an imidazole nitrogen (say) to be 2.4 Angstroms away from an iron atom in a heme group, or a methyl group to be 3.0 Angstroms from the same atom, and not WITHIN a radius of this distance, since it can be anywhere from 0 to the distance I want, and lead to situations I'm seeing now, where the molecule I'm docking is on top of the heme. TIA, Richard