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--