From owner-chemistry@ccl.net Fri Nov 2 08:42:01 2012 From: "John McKelvey jmmckel-*-gmail.com" To: CCL Subject: CCL: Linux performance using a VM appliance Message-Id: <-47830-121102084129-14588-IKE4k+9FV/l1Yp0zDj91Qw .. server.ccl.net> X-Original-From: John McKelvey Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 2 Nov 2012 08:41:23 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel##gmail.com] Hello.. Does anyone have experience running linux QM codes using a Virtual Machine under Windows? What is your estimate of efficiency using a V M relative to native code? Many thanks, John -- John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel---gmail.com From owner-chemistry@ccl.net Fri Nov 2 09:17:00 2012 From: "Ashley Chen huijia_15---yahoo.com" To: CCL Subject: CCL:G: Obtaining parameters for ONIOM calculations in Gaussian Message-Id: <-47831-121101035052-8162-aJeq1lbrZLMLtbyzuefOHA:+:server.ccl.net> X-Original-From: "Ashley Chen " Date: Thu, 1 Nov 2012 03:50:51 -0400 Sent to CCL by: "Ashley Chen " [huijia_15++yahoo.com] Hi, I am trying to run ONIOM calculations in Gaussian but I have gotten error in the output file. Angle bend undefined between atoms 5294 5295 5297 Angle bend undefined between atoms 5294 5308 5299 Angle bend undefined between atoms 5294 5308 5306 Angle bend undefined between atoms 5295 5297 5298 Angle bend undefined between atoms 5295 5297 5299 Angle bend undefined between atoms 5296 5295 5297 Angle bend undefined between atoms 5297 5299 5308 Angle bend undefined between atoms 5300 5299 5308 Angle bend undefined between atoms 5302 5304 5305 Angle bend undefined between atoms 5302 5304 5306 MM function not complete I found out that I have to input the following into the input file but I am not sure where can I obtain such information. Can anyone help me on this? Hrmstr1 CM N2 0.0000 0.0000 HrmBnd1 CT CT CM 63.0000 111.0000 HrmBnd1 CT CM CA 0.0000 0.0000 HrmBnd1 CM CM N2 0.0000 0.0000 HrmBnd1 CM CA CA 0.0000 0.0000 HrmBnd1 CM N2 H 0.0000 0.0000 HrmBnd1 CM N2 CA 0.0000 0.0000 HrmBnd1 H4 CM N2 0.0000 0.0000 HrmBnd1 N2 CA CA 66.8000 119.5700 HrmBnd1 CM CA HA 0.0000 0.0000 HrmBnd1 CT CM N2 0.0000 0.0000 HrmBnd1 CM N2 CM 0.0000 0.0000 HrmBnd1 N2 CM H5 0.0000 0.0000 HrmBnd1 N2 CM N2 0.0000 0.0000 I tried to deduce these information from amber.prm file but the above paramters were not found. Thank you so much for your help. Regards, Ashley From owner-chemistry@ccl.net Fri Nov 2 09:52:00 2012 From: "Ashley Chen huijia_15(~)yahoo.com" To: CCL Subject: CCL:G: Obtaining parameters for ONIOM calculations in Gaussian Message-Id: <-47832-121102023712-23107-IjGPtZdnRh5hn9Pq31LHhA%a%server.ccl.net> X-Original-From: "Ashley Chen" Date: Fri, 2 Nov 2012 02:37:11 -0400 Sent to CCL by: "Ashley Chen" [huijia_15\a/yahoo.com] Hi, I am trying to run ONIOM calculations in Gaussian but I have gotten error in the output file. Angle bend undefined between atoms 5294 5295 5297 Angle bend undefined between atoms 5294 5308 5299 Angle bend undefined between atoms 5294 5308 5306 Angle bend undefined between atoms 5295 5297 5298 Angle bend undefined between atoms 5295 5297 5299 Angle bend undefined between atoms 5296 5295 5297 Angle bend undefined between atoms 5297 5299 5308 Angle bend undefined between atoms 5300 5299 5308 Angle bend undefined between atoms 5302 5304 5305 Angle bend undefined between atoms 5302 5304 5306 MM function not complete I found out that I have to input the following into the input file but I am not sure where can I obtain such information. Can anyone help me on this? Hrmstr1 CM N2 0.0000 0.0000 HrmBnd1 CT CT CM 63.0000 111.0000 HrmBnd1 CT CM CA 0.0000 0.0000 HrmBnd1 CM CM N2 0.0000 0.0000 HrmBnd1 CM CA CA 0.0000 0.0000 HrmBnd1 CM N2 H 0.0000 0.0000 HrmBnd1 CM N2 CA 0.0000 0.0000 HrmBnd1 H4 CM N2 0.0000 0.0000 HrmBnd1 N2 CA CA 66.8000 119.5700 HrmBnd1 CM CA HA 0.0000 0.0000 HrmBnd1 CT CM N2 0.0000 0.0000 HrmBnd1 CM N2 CM 0.0000 0.0000 HrmBnd1 N2 CM H5 0.0000 0.0000 HrmBnd1 N2 CM N2 0.0000 0.0000 I tried to deduce these information from amber.prm file but the above paramters were not found. Thank you so much for your help. Regards, Ashley From owner-chemistry@ccl.net Fri Nov 2 14:03:00 2012 From: "Lee Shekter lshekter^^gmail.com" To: CCL Subject: CCL: Compiling GAMESS 1 MAY 2012 Linux Mint 13 Message-Id: <-47833-121102111546-23330-fNepvFDDrYlCO3lYNImSxg*server.ccl.net> X-Original-From: "Lee Shekter" Date: Fri, 2 Nov 2012 11:15:45 -0400 Sent to CCL by: "Lee Shekter" [lshekter|,|gmail.com] I have a problem in the final step of linking GAMESS, 1 MAY 2012, OS Linux Mint 13 on a Dell Optiplex 760 Desktop. I have no problems compiling and linking on Ubuntu 12.04 (precise pangolin) on a different machine. The problem is in the final linking step. This is the error: The message passing libraries searched are /usr/local/gamess/ddi/libddi.a -lpthread Other libraries, including math libraries, to be searched are -L/usr/lib/atlas-base/atlas -lf77blas -latlas Linker messages (if any) follow... /usr/bin/ld: cannot find -lf77blas /usr/bin/ld: cannot find -latlas collect2: ld returned 1 exit status Unfortunately, there was an error while linking GAMESS. Has anyone else tried to compile GAMESS (or other software) on Linux Mint and run into this problem? A web search revealed that people have had similar problems with other code, just not with GAMESS, that I could find. Thank you. From owner-chemistry@ccl.net Fri Nov 2 16:53:00 2012 From: "Clarke Earley cearley_-_kent.edu" To: CCL Subject: CCL: Compiling GAMESS 1 MAY 2012 Linux Mint 13 Message-Id: <-47834-121102150347-9041-lL7vcbgCHmBj2GbKmqlb9g^-^server.ccl.net> X-Original-From: Clarke Earley Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 02 Nov 2012 15:03:37 -0400 MIME-Version: 1.0 Sent to CCL by: Clarke Earley [cearley(0)kent.edu] Lee, While I haven't tried this on Linux Mint, on Debian I have had success using the following path for atlas. /usr/lib64/atlas-base/ Good luck with this. Clarke On 11/02/2012 11:15 AM, Lee Shekter lshekter^^gmail.com wrote: > Sent to CCL by: "Lee Shekter" [lshekter|,|gmail.com] > I have a problem in the final step of linking GAMESS, 1 MAY 2012, OS Linux Mint > 13 on a Dell Optiplex 760 Desktop. I have no problems compiling and linking on > Ubuntu 12.04 (precise pangolin) on a different machine. The problem is in the > final linking step. This is the error: > > The message passing libraries searched are > /usr/local/gamess/ddi/libddi.a -lpthread > > Other libraries, including math libraries, to be searched are > -L/usr/lib/atlas-base/atlas -lf77blas -latlas > > Linker messages (if any) follow... > /usr/bin/ld: cannot find -lf77blas > /usr/bin/ld: cannot find -latlas > collect2: ld returned 1 exit status > > Unfortunately, there was an error while linking GAMESS. > > Has anyone else tried to compile GAMESS (or other software) on Linux Mint and > run into this problem? A web search revealed that people have had similar > problems with other code, just not with GAMESS, that I could find. Thank you.