From owner-nwchem-users@emsl.pnl.gov Tue Nov 21 17:46:34 2006 Received: from odyssey.emsl.pnl.gov (localhost [127.0.0.1]) by odyssey.emsl.pnl.gov (8.13.8/8.13.8) with ESMTP id kAM1kXvb002234 for ; Tue, 21 Nov 2006 17:46:34 -0800 (PST) Received: (from majordom@localhost) by odyssey.emsl.pnl.gov (8.13.8/8.13.8/Submit) id kAM1kXjs002233 for nwchem-users-outgoing-0915; Tue, 21 Nov 2006 17:46:33 -0800 (PST) X-Authentication-Warning: odyssey.emsl.pnl.gov: majordom set sender to owner-nwchem-users@emsl.pnl.gov using -f X-IronPort-AV: i="4.09,445,1157353200"; d="scan'208"; a="8608666:sNHT33399779" X-MimeOLE: Produced By Microsoft Exchange V6.5 Content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Subject: [NWCHEM] NWChem QHOP Date: Tue, 21 Nov 2006 17:46:30 -0800 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: NWChem QHOP Thread-Index: AccN2AgxfaPmEXdRQOKwW4s21LAgig== From: "Venkatnathan, Arun" To: X-OriginalArrivalTime: 22 Nov 2006 01:46:31.0312 (UTC) FILETIME=[08AED100:01C70DD8] Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by odyssey.emsl.pnl.gov id kAM1kWt2002230 Sender: owner-nwchem-users@emsl.pnl.gov Precedence: bulk Dear NWChem Users, I am trying to use QHOP in NWChem MD. I am trying to create a topology file for qhop by modifying protonation sites on the molecule using the prepare module. I will deeply appreciate if QHOP users in NWChem can share a sample .nw script file and PDB file which shows how to use the keywords "modify segment n protonation m" and "qhop" in proper way or any other keywords qhop requires to perform a MD simulation. Thanks in advance, - Arun -