From owner-chemistry@ccl.net Tue Jul 20 01:18:00 2010 From: "Wo Agenssi witch.of.agnessi(!)gmail.com" To: CCL Subject: CCL: Whether atom belongs to H-bond Donor, acceptor or both:Any Freeware? Message-Id: <-42311-100720011458-17443-r8LTHNWz8Xpd1vUHsYy0Fw^^^server.ccl.net> X-Original-From: "Wo Agenssi" Date: Tue, 20 Jul 2010 01:14:57 -0400 Sent to CCL by: "Wo Agenssi" [witch.of.agnessi^gmail.com] Dear CCLers, I need to know whether the atoms of a group of ligands belong to Hydrogen bond donor, acceptor or both. In addition I also need to know in how many H- bonds the particular atom can participate. Please let me know if there are some freewares to do this job Thanks in advance WoA From owner-chemistry@ccl.net Tue Jul 20 09:30:01 2010 From: "Vladimir Potapov vladimir.potapov : gmail.com" To: CCL Subject: CCL: Whether atom belongs to H-bond Donor, acceptor or both:Any Freeware? Message-Id: <-42312-100720052659-24730-Y9hWNwgDdo39wiKgbKz+LQ..server.ccl.net> X-Original-From: Vladimir Potapov Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 20 Jul 2010 12:26:08 +0300 MIME-Version: 1.0 Sent to CCL by: Vladimir Potapov [vladimir.potapov[a]gmail.com] Hi WoA, You can try to look at LPC software (Ligand-Protein Contacts): Publication: Automated analysis of interatomic contacts in proteins. Sobolev et al. Bioinformatics. 1999 Apr; 15(4):327-32. Web site: http://ligin.weizmann.ac.il/space/programs/ The goal of the software is to calculate contacts between a ligand and a protein. Classification of ligand atoms is a part of the program. Maybe you can adjust it to your needs. Regards, Vladimir On Tue, Jul 20, 2010 at 8:14 AM, Wo Agenssi witch.of.agnessi(!)gmail.com wrote: > > Sent to CCL by: "Wo  Agenssi" [witch.of.agnessi^gmail.com] > Dear CCLers, > > I need to know whether the atoms of a group of ligands belong to Hydrogen > bond donor, acceptor or both. In addition I also need to know in how many H- > bonds the particular atom can participate. > > Please let me know if there are some freewares to do this job > > Thanks in advance > > WoA From owner-chemistry@ccl.net Tue Jul 20 15:48:00 2010 From: "Adam Tenderholt atenderholt^gmail.com" To: CCL Subject: CCL:G: install g98 in ubuntu Message-Id: <-42313-100720152609-12687-bP80qyjeyaNQQXdqqsnzsg%a%server.ccl.net> X-Original-From: Adam Tenderholt Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 20 Jul 2010 12:25:40 -0700 MIME-Version: 1.0 Sent to CCL by: Adam Tenderholt [atenderholt**gmail.com] Hi Yuniawan, Hopefully someone has already replied to you, but if you're still having problems, it's because your g98root is incorrect. Try the following: export GAUSS_SCRDIR=$GAUSS_SCRDIR:/tmp g98root=/usr/local export g98root source $g98root/g98/bsd/g98.profile Note that this assumes the g98 executable is located in /usr/local/ and NOT in /usr/local/g98/. If it's really in the latter, then you'll need g98root=/usr/local/g98. Adam On Sun, Jul 18, 2010 at 5:47 PM, yuniawan hidayat yuniawan.hidayat]_[yahoo.com wrote: > > Sent to CCL by: "yuniawan  hidayat" [yuniawan.hidayat.:.yahoo.com] > Dear all > I'm stuck installing g98 in ubuntu. I have set environment for g98 in .profile and bash.hrc like this : > > export PATH=$PATH:/usr/local/g98 > export GAUSS_SCRDIR=$GAUSS_SCRDIR:/tmp > g98root=/home/masiwan > export g98root > . $g98root/g98/bsd/g98.profile > > I have install g98 in /usr/local, but when I run "g98 file.con &" but always get message "bash: g98: command not found" > > can you help to show me installing g98 in ubuntu step by step? > > thanks...>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > > From owner-chemistry@ccl.net Tue Jul 20 21:34:01 2010 From: "Brian Salter-Duke Brian.James.Duke[]gmail.com" To: CCL Subject: CCL:G: install g98 in ubuntu Message-Id: <-42314-100720184237-12974-O94Snn+rO+ShSnqXfe7hxQ*_*server.ccl.net> X-Original-From: Brian Salter-Duke Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Wed, 21 Jul 2010 08:41:39 +1000 MIME-Version: 1.0 Sent to CCL by: Brian Salter-Duke [Brian.James.Duke:-:gmail.com] On Tue, Jul 20, 2010 at 12:25:40PM -0700, Adam Tenderholt atenderholt^gmail.com wrote: > > Sent to CCL by: Adam Tenderholt [atenderholt**gmail.com] > Hi Yuniawan, > > Hopefully someone has already replied to you, but if you're still > having problems, it's because your g98root is incorrect. Try the > following: > > export GAUSS_SCRDIR=$GAUSS_SCRDIR:/tmp This is wrong. $GAUSS_SCRDIR is not a path. It should point to a single place - the scratch directory. That is:- export GAUSS_SCRDIR=/tmp > g98root=/usr/local > export g98root > source $g98root/g98/bsd/g98.profile > > Note that this assumes the g98 executable is located in /usr/local/ > and NOT in /usr/local/g98/. If it's really in the latter, then you'll > need g98root=/usr/local/g98. This is also wrong. If $g98root is /usr/local/ then the gaussuan directory is /usr/local/g98/ and the g98 executable is /usr/local/g98/g98 and the links are. e.g. /usr/local/g98/l101.exe. g98root=/usr/local/g98 would put the executable at g98root=/usr/local/g98/g98/g98. Look at: source $g98root/g98/bsd/g98.profile g98.profile is a file in directory bsd which is in directory g98. The executable 'g98' is at the same level as bsd. Brian. > Adam > > > On Sun, Jul 18, 2010 at 5:47 PM, yuniawan hidayat > yuniawan.hidayat]_[yahoo.com wrote: > > > > Sent to CCL by: "yuniawan  hidayat" [yuniawan.hidayat.:.yahoo.com] > > Dear all > > I'm stuck installing g98 in ubuntu. I have set environment for g98 in .profile and bash.hrc like this : > > > > export PATH=$PATH:/usr/local/g98 > > export GAUSS_SCRDIR=$GAUSS_SCRDIR:/tmp > > g98root=/home/masiwan > > export g98root > > . $g98root/g98/bsd/g98.profile > > > > I have install g98 in /usr/local, but when I run "g98 file.con &" but always get message "bash: g98: command not found" > > > > can you help to show me installing g98 in ubuntu step by step? > > > > thanks...>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> -- Brian Salter-Duke (Brian Duke) Brian.Salter-Duke!=!monash.edu Honorary Researcher Fellow Monash Institute of Pharmaceutical Sciences, Monash University Parkville Campus, VIC 3052, Australia.