From owner-chemistry@ccl.net Wed Nov 16 06:10:01 2011 From: "Joseph Tucker joe.tucker]=[scienomics.com" To: CCL Subject: CCL: GCMC isotherms Message-Id: <-45886-111116060819-21169-vOntKgbH9IhzCLCLAAiPoA#,#server.ccl.net> X-Original-From: "Joseph Tucker" Date: Wed, 16 Nov 2011 06:08:16 -0500 Sent to CCL by: "Joseph Tucker" [joe.tucker|,|scienomics.com] 1) I am not aware of an other open source software 2) I am not aware of how GULP operates 3) For Towhee, the chemical potential should be calculated in the gas/liquid phase using Widom scheme. It is important to do so since the value is connected with the force field applied. For this reason: a) you prepare the initial configuration b) relax non-bonded interactions applying a minimization scheme c) perform a NPT simulation to relax the density d) perform a NPT simulation using also Widom insertion to calculate the chemical potential The result will be the chemical potential for the T and P conditions in used. Now you are able to setup a CGMC since you have (T,P). Towhee use as input the total chemical potential while other software uses the excess chemical potential. The two approaches are equivalent. For Towhee, take a look at the manual for the chemical potential definition in use. Also take a look at this paper by my colleague Giorgos: Adsorption of N2, CH4, CO and CO2 gases in single walled carbon nanotubes: A combined experimental and Monte Carlo molecular simulation study Lithoxoos, G.P , Labropoulos, A., Peristeras, L.D , Kanellopoulos, N , Samios, Economou, I.G. Journal of Supercritical Fluids Volume 55, Issue 2, December 2010, Pages 510-523 From owner-chemistry@ccl.net Wed Nov 16 08:06:00 2011 From: "divya neelagiri divya.neelagiri0*o*gmail.com" To: CCL Subject: CCL: tinker Message-Id: <-45887-111115224031-7960-P3pW5FHh/kt/o+GtubpMsA^-^server.ccl.net> X-Original-From: divya neelagiri Content-Type: multipart/alternative; boundary=bcaec554e08c22c2b104b1d1ddb5 Date: Tue, 15 Nov 2011 22:40:02 -0500 MIME-Version: 1.0 Sent to CCL by: divya neelagiri [divya.neelagiri0(_)gmail.com] --bcaec554e08c22c2b104b1d1ddb5 Content-Type: text/plain; charset=ISO-8859-1 Respected sir/madam, I am currently working on a project for which I need to use tinker. When I tried to find general confirmational analysis for small molecules I got this error. I tried all the parameter files. I understood that I have some missing parameters but I dont understand how I can get them or where I can get them from. Any help in this matter would be great. I also sent an attachment which has entire execution. Please reply back with some solution. And can you please tell me how I can install FFE for GUI for tinker. MECHANIC -- Some Required Potential Energy Parameters are Undefined TINKER is Unable to Continue; Terminating the Current Calculation This is the complete error message. [divya|a|dvs04 outputs_mol2_sdf]$ scan ############################################################################## ############################################################################## ## ## ## TINKER --- Software Tools for Molecular Design ## ## ## ## Version 5.1 February 2010 ## ## ## ## Copyright (c) Jay William Ponder 1990-2010 ## ## All Rights Reserved ## ## ## ############################################################################## ############################################################################## Enter Cartesian Coordinate File Name : alkane.xyz Enter Potential Parameter File Name : /data2/pgm/tinker/params/mm2.prm Selection of Torsional Angles for Rotation : 0 - Automatic Selection of Torsional Angles 1 - Manual Selection of Angles to Rotate 2 - Manual Selection of Angles to Freeze Enter the Method of Choice [0] : 0 Number of Torsions Used in Derivative Computation : 38 Enter the Number Search Directions for Local Search [5] : 5 Enter the Energy Threshold for Local Minima [100.0] : 100 Enter RMS Gradient per Atom Criterion [0.0001] : 0.0001 Generating Seed Point for Potential Energy Surface Scan Potential Surface Map Minimum 1 24.4783 Normal Mode Local Search Minimum 1 forrtl: error (69): process interrupted (SIGINT) Image PC Routine Line Source scan 080A2A82 Unknown Unknown Unknown scan 080A1832 Unknown Unknown Unknown scan 080A039B Unknown Unknown Unknown scan 0804A025 Unknown Unknown Unknown scan 080492D5 Unknown Unknown Unknown scan 08048261 Unknown Unknown Unknown scan 0828D8F8 Unknown Unknown Unknown scan 08048131 Unknown Unknown Unknown [divya|a|dvs04 outputs_mol2_sdf]$ scan ############################################################################## ############################################################################## ## ## ## TINKER --- Software Tools for Molecular Design ## ## ## ## Version 5.1 February 2010 ## ## ## ## Copyright (c) Jay William Ponder 1990-2010 ## ## All Rights Reserved ## ## ## ############################################################################## ############################################################################## Enter Cartesian Coordinate File Name : test1.txyz Enter Potential Parameter File Name : /data2/pgm/tinker/params/mm2.prm Atoms with an Unusual Number of Attached Atoms : Type Atom Name Atom Type Expected Found Valence 8-N 9 3 2 Valence 10-O 7 1 2 Valence 11-N 9 3 2 Valence 20-O 6 4 2 Valence 26-N 8 4 3 Undefined Bond Stretching Parameters : Type Atom Names Atom Classes Bond 3-C 23-S 2 18 Bond 9-C 10-O 2 7 Bond 10-O 11-N 7 9 Bond 12-C 13-O 2 7 Bond 14-N 37-H 9 5 Bond 17-N 62-H 8 5 Bond 23-S 26-N 18 8 Undefined Angle Bending Parameters : Type Atom Names Atom Classes Angle 2-C 3-C 23-S 2 2 18 Angle 4-C 3-C 23-S 2 2 18 Angle 8-N 9-C 10-O 9 2 7 Angle 10-O 9-C 12-C 7 2 2 Angle 9-C 10-O 11-N 2 7 9 Angle 7-C 11-N 10-O 2 9 7 Angle 9-C 12-C 13-O 2 2 7 Angle 13-O 12-C 14-N 7 2 9 Angle 12-C 14-N 37-H 2 9 5 Angle 15-C 14-N 37-H 1 9 5 Angle 16-C 17-N 62-H 1 8 5 Angle 18-C 17-N 62-H 1 8 5 Angle 22-C 17-N 62-H 1 8 5 Angle 3-C 23-S 24-O 2 18 7 Angle 3-C 23-S 25-O 2 18 7 Angle 3-C 23-S 26-N 2 18 8 Angle 24-O 23-S 26-N 7 18 8 Angle 25-O 23-S 26-N 7 18 8 Angle 23-S 26-N 27-C 18 8 1 Angle 23-S 26-N 32-C 18 8 1 Undefined Out-of-Plane Bend Parameters : Type Atom Names Atom Classes Angle-OP 23-S 3-C 2-C 4-C 18 2 2 2 Angle-OP 37-H 14-N 12-C 15-C 5 9 2 1 Undefined Torsional Parameters : Type Atom Names Atom Classes Torsion 1-C 2-C 3-C 23-S 2 2 2 18 Torsion 34-H 2-C 3-C 23-S 5 2 2 18 Torsion 23-S 3-C 4-C 5-C 18 2 2 2 Torsion 23-S 3-C 4-C 35-H 18 2 2 5 Torsion 2-C 3-C 23-S 24-O 2 2 18 7 Torsion 2-C 3-C 23-S 25-O 2 2 18 7 Torsion 2-C 3-C 23-S 26-N 2 2 18 8 Torsion 4-C 3-C 23-S 24-O 2 2 18 7 Torsion 4-C 3-C 23-S 25-O 2 2 18 7 Torsion 4-C 3-C 23-S 26-N 2 2 18 8 Torsion 11-N 7-C 8-N 9-C 9 2 9 2 Torsion 6-C 7-C 11-N 10-O 2 2 9 7 Torsion 8-N 7-C 11-N 10-O 9 2 9 7 Torsion 7-C 8-N 9-C 10-O 2 9 2 7 Torsion 8-N 9-C 10-O 11-N 9 2 7 9 Torsion 12-C 9-C 10-O 11-N 2 2 7 9 Torsion 8-N 9-C 12-C 13-O 9 2 2 7 Torsion 8-N 9-C 12-C 14-N 9 2 2 9 Torsion 10-O 9-C 12-C 13-O 7 2 2 7 Torsion 10-O 9-C 12-C 14-N 7 2 2 9 Torsion 9-C 10-O 11-N 7-C 2 7 9 2 Torsion 9-C 12-C 14-N 37-H 2 2 9 5 Torsion 13-O 12-C 14-N 15-C 7 2 9 1 Torsion 13-O 12-C 14-N 37-H 7 2 9 5 Torsion 37-H 14-N 15-C 16-C 5 9 1 1 Torsion 37-H 14-N 15-C 38-H 5 9 1 5 Torsion 37-H 14-N 15-C 39-H 5 9 1 5 Torsion 15-C 16-C 17-N 62-H 1 1 8 5 Torsion 40-H 16-C 17-N 62-H 5 1 8 5 Torsion 41-H 16-C 17-N 62-H 5 1 8 5 Torsion 62-H 17-N 18-C 19-C 5 8 1 1 Torsion 62-H 17-N 18-C 42-H 5 8 1 5 Torsion 62-H 17-N 18-C 43-H 5 8 1 5 Torsion 62-H 17-N 22-C 21-C 5 8 1 1 Torsion 62-H 17-N 22-C 48-H 5 8 1 5 Torsion 62-H 17-N 22-C 49-H 5 8 1 5 Torsion 3-C 23-S 26-N 27-C 2 18 8 1 Torsion 3-C 23-S 26-N 32-C 2 18 8 1 Torsion 24-O 23-S 26-N 27-C 7 18 8 1 Torsion 24-O 23-S 26-N 32-C 7 18 8 1 Torsion 25-O 23-S 26-N 27-C 7 18 8 1 Torsion 25-O 23-S 26-N 32-C 7 18 8 1 Torsion 23-S 26-N 27-C 28-C 18 8 1 1 Torsion 23-S 26-N 27-C 50-H 18 8 1 5 Torsion 23-S 26-N 27-C 51-H 18 8 1 5 Torsion 23-S 26-N 32-C 31-C 18 8 1 1 Torsion 23-S 26-N 32-C 60-H 18 8 1 5 Torsion 23-S 26-N 32-C 61-H 18 8 1 5 MECHANIC -- Some Required Potential Energy Parameters are Undefined TINKER is Unable to Continue; Terminating the Current Calculation Thank you, Divya --bcaec554e08c22c2b104b1d1ddb5 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: base64 UmVzcGVjdGVkIHNpci9tYWRhbSw8YnI+PGJyPqCgoKCgoKCgoKCgoKCgIEkgYW0gY3VycmVudGx5 IHdvcmtpbmcgb24gYSBwcm9qZWN0IGZvciB3aGljaCBJIG5lZWQgdG8gdXNlIHRpbmtlci4gV2hl biBJIHRyaWVkIHRvIGZpbmQgZ2VuZXJhbCBjb25maXJtYXRpb25hbCBhbmFseXNpcyBmb3Igc21h bGwgbW9sZWN1bGVzIEkgZ290IHRoaXMgZXJyb3IuIEkgdHJpZWQgYWxsIHRoZSBwYXJhbWV0ZXIg ZmlsZXMuIEkgdW5kZXJzdG9vZCB0aGF0IEkgaGF2ZSBzb21lIG1pc3NpbmcgcGFyYW1ldGVycyBi dXQgSSBkb250IHVuZGVyc3RhbmQgaG93IEkgY2FuIGdldCB0aGVtIG9yIHdoZXJlIEkgY2FuIGdl dCB0aGVtIGZyb20uIEFueSBoZWxwIGluIHRoaXMgbWF0dGVyIHdvdWxkIGJlIGdyZWF0LiBJIGFs 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MjMtU6CgoKCgIDI2LU6goKCgoCAzMi1DoKCgoKAgNjAtSKCgoKCgoKCgoCAxOKCgoCA4oKCgIDGg oKAgNTxicj4KCqBUb3JzaW9uoKCgoKCgoCAyMy1ToKCgoKAgMjYtTqCgoKCgIDMyLUOgoKCgoCA2 MS1IoKCgoKCgoKCgIDE4oKCgIDigoKAgMaCgoCA1PGJyPjxicj6gTUVDSEFOSUOgIC0toCBTb21l IFJlcXVpcmVkIFBvdGVudGlhbCBFbmVyZ3kgUGFyYW1ldGVycyBhcmUgVW5kZWZpbmVkPGJyPjxi cj6gVElOS0VSIGlzIFVuYWJsZSB0byBDb250aW51ZTsgVGVybWluYXRpbmcgdGhlIEN1cnJlbnQg Q2FsY3VsYXRpb248YnI+Cgo8YnI+PGJyPlRoYW5rIHlvdSw8YnI+RGl2eWE8YnI+Cg== --bcaec554e08c22c2b104b1d1ddb5-- From owner-chemistry@ccl.net Wed Nov 16 12:04:01 2011 From: "VALVERDE CARRILLO, JOSE RAMON jrvalverde##cnb.csic.es" To: CCL Subject: CCL: tinker Message-Id: <-45888-111116120113-15660-5dsmcS9Ycgl/xCm0IsNF1w..server.ccl.net> X-Original-From: "VALVERDE CARRILLO, JOSE RAMON" Content-Transfer-Encoding: 7bit Content-Type: multipart/alternative; boundary="=_75sv1wgpgsb3" Date: Wed, 16 Nov 2011 18:01:03 +0100 MIME-Version: 1.0 Sent to CCL by: "VALVERDE CARRILLO, JOSE RAMON" [jrvalverde]|[cnb.csic.es] This message is in MIME format. --=_75sv1wgpgsb3 Content-Type: text/plain; charset=UTF-8 Content-Description: =?utf-8?b?VmVyc2nDs24=?= de texto del mensaje Content-Disposition: inline Content-Transfer-Encoding: 7bit It is most likely because you have atoms in your input file that are not recognised by the parameter/force field you selected. This may be due to differences in force field atom naming conventions. Identify the atoms that give you the trouble and fix their names. A second possibility is that your geometry is plainly wrong, and thus tinker complains that it does not correspond to what is coherent with the atomic paramters it has. It might be because you are using the wrong units and it build a wrong connectivity or because you actually introduced a weird geometry. Quoting "divya neelagiri divya.neelagiri0*o*gmail.com": > Respected sir/madam, > > I am currently working on a project for which I need to use > tinker. When I tried to find general confirmational analysis for small > molecules I got this error. I tried all the parameter files. I understood > that I have some missing parameters but I dont understand how I can get > them or where I can get them from. Any help in this matter would be great. > I also sent an attachment which has entire execution. Please reply back > with some solution. And can you please tell me how I can install FFE for > GUI for tinker. > > > MECHANIC -- Some Required Potential Energy Parameters are Undefined > > TINKER is Unable to Continue; Terminating the Current Calculation > > > > > This is the complete error message. > > > > > > [divya%%dvs04 outputs_mol2_sdf]$ scan > > > ############################################################################## > > ############################################################################## > ## > ## > ## TINKER --- Software Tools for Molecular > Design ## > ## > ## > ## Version 5.1 February > 2010 ## > ## > ## > ## Copyright (c) Jay William Ponder > 1990-2010 ## > ## All Rights > Reserved ## > ## > ## > > ############################################################################## > > ############################################################################## > > > Enter Cartesian Coordinate File Name : alkane.xyz > > Enter Potential Parameter File Name : /data2/pgm/tinker/params/mm2.prm > > Selection of Torsional Angles for Rotation : > > 0 - Automatic Selection of Torsional Angles > 1 - Manual Selection of Angles to Rotate > 2 - Manual Selection of Angles to Freeze > > Enter the Method of Choice [0] : 0 > > Number of Torsions Used in Derivative Computation : 38 > > Enter the Number Search Directions for Local Search [5] : 5 > > Enter the Energy Threshold for Local Minima [100.0] : 100 > > Enter RMS Gradient per Atom Criterion [0.0001] : 0.0001 > > Generating Seed Point for Potential Energy Surface Scan > > > Potential Surface Map Minimum 1 24.4783 > > > Normal Mode Local Search Minimum 1 > > forrtl: error (69): process interrupted (SIGINT) > Image PC Routine Line > Source > scan 080A2A82 Unknown Unknown Unknown > scan 080A1832 Unknown Unknown Unknown > scan 080A039B Unknown Unknown Unknown > scan 0804A025 Unknown Unknown Unknown > scan 080492D5 Unknown Unknown Unknown > scan 08048261 Unknown Unknown Unknown > scan 0828D8F8 Unknown Unknown Unknown > scan 08048131 Unknown Unknown Unknown > [divya%%dvs04 outputs_mol2_sdf]$ scan > > > ############################################################################## > > ############################################################################## > ## > ## > ## TINKER --- Software Tools for Molecular > Design ## > ## > ## > ## Version 5.1 February > 2010 ## > ## > ## > ## Copyright (c) Jay William Ponder > 1990-2010 ## > ## All Rights > Reserved ## > ## > ## > > ############################################################################## > > ############################################################################## > > > Enter Cartesian Coordinate File Name : test1.txyz > > Enter Potential Parameter File Name : /data2/pgm/tinker/params/mm2.prm > > Atoms with an Unusual Number of Attached Atoms : > > Type Atom Name Atom Type Expected Found > > Valence 8-N 9 3 2 > Valence 10-O 7 1 2 > Valence 11-N 9 3 2 > Valence 20-O 6 4 2 > Valence 26-N 8 4 3 > > Undefined Bond Stretching Parameters : > > Type Atom Names Atom Classes > > Bond 3-C 23-S 2 18 > Bond 9-C 10-O 2 7 > Bond 10-O 11-N 7 9 > Bond 12-C 13-O 2 7 > Bond 14-N 37-H 9 5 > Bond 17-N 62-H 8 5 > Bond 23-S 26-N 18 8 > > Undefined Angle Bending Parameters : > > Type Atom Names Atom Classes > > Angle 2-C 3-C 23-S 2 2 18 > Angle 4-C 3-C 23-S 2 2 18 > Angle 8-N 9-C 10-O 9 2 7 > Angle 10-O 9-C 12-C 7 2 2 > Angle 9-C 10-O 11-N 2 7 9 > Angle 7-C 11-N 10-O 2 9 7 > Angle 9-C 12-C 13-O 2 2 7 > Angle 13-O 12-C 14-N 7 2 9 > Angle 12-C 14-N 37-H 2 9 5 > Angle 15-C 14-N 37-H 1 9 5 > Angle 16-C 17-N 62-H 1 8 5 > Angle 18-C 17-N 62-H 1 8 5 > Angle 22-C 17-N 62-H 1 8 5 > Angle 3-C 23-S 24-O 2 18 7 > Angle 3-C 23-S 25-O 2 18 7 > Angle 3-C 23-S 26-N 2 18 8 > Angle 24-O 23-S 26-N 7 18 8 > Angle 25-O 23-S 26-N 7 18 8 > Angle 23-S 26-N 27-C 18 8 1 > Angle 23-S 26-N 32-C 18 8 1 > > Undefined Out-of-Plane Bend Parameters : > > Type Atom Names Atom Classes > > Angle-OP 23-S 3-C 2-C 4-C 18 2 2 > 2 > Angle-OP 37-H 14-N 12-C 15-C 5 9 2 > 1 > > Undefined Torsional Parameters : > > Type Atom Names Atom Classes > > Torsion 1-C 2-C 3-C 23-S 2 2 2 > 18 > Torsion 34-H 2-C 3-C 23-S 5 2 2 > 18 > Torsion 23-S 3-C 4-C 5-C 18 2 2 > 2 > Torsion 23-S 3-C 4-C 35-H 18 2 2 > 5 > Torsion 2-C 3-C 23-S 24-O 2 2 18 > 7 > Torsion 2-C 3-C 23-S 25-O 2 2 18 > 7 > Torsion 2-C 3-C 23-S 26-N 2 2 18 > 8 > Torsion 4-C 3-C 23-S 24-O 2 2 18 > 7 > Torsion 4-C 3-C 23-S 25-O 2 2 18 > 7 > Torsion 4-C 3-C 23-S 26-N 2 2 18 > 8 > Torsion 11-N 7-C 8-N 9-C 9 2 9 > 2 > Torsion 6-C 7-C 11-N 10-O 2 2 9 > 7 > Torsion 8-N 7-C 11-N 10-O 9 2 9 > 7 > Torsion 7-C 8-N 9-C 10-O 2 9 2 > 7 > Torsion 8-N 9-C 10-O 11-N 9 2 7 > 9 > Torsion 12-C 9-C 10-O 11-N 2 2 7 > 9 > Torsion 8-N 9-C 12-C 13-O 9 2 2 > 7 > Torsion 8-N 9-C 12-C 14-N 9 2 2 > 9 > Torsion 10-O 9-C 12-C 13-O 7 2 2 > 7 > Torsion 10-O 9-C 12-C 14-N 7 2 2 > 9 > Torsion 9-C 10-O 11-N 7-C 2 7 9 > 2 > Torsion 9-C 12-C 14-N 37-H 2 2 9 > 5 > Torsion 13-O 12-C 14-N 15-C 7 2 9 > 1 > Torsion 13-O 12-C 14-N 37-H 7 2 9 > 5 > Torsion 37-H 14-N 15-C 16-C 5 9 1 > 1 > Torsion 37-H 14-N 15-C 38-H 5 9 1 > 5 > Torsion 37-H 14-N 15-C 39-H 5 9 1 > 5 > Torsion 15-C 16-C 17-N 62-H 1 1 8 > 5 > Torsion 40-H 16-C 17-N 62-H 5 1 8 > 5 > Torsion 41-H 16-C 17-N 62-H 5 1 8 > 5 > Torsion 62-H 17-N 18-C 19-C 5 8 1 > 1 > Torsion 62-H 17-N 18-C 42-H 5 8 1 > 5 > Torsion 62-H 17-N 18-C 43-H 5 8 1 > 5 > Torsion 62-H 17-N 22-C 21-C 5 8 1 > 1 > Torsion 62-H 17-N 22-C 48-H 5 8 1 > 5 > Torsion 62-H 17-N 22-C 49-H 5 8 1 > 5 > Torsion 3-C 23-S 26-N 27-C 2 18 8 > 1 > Torsion 3-C 23-S 26-N 32-C 2 18 8 > 1 > Torsion 24-O 23-S 26-N 27-C 7 18 8 > 1 > Torsion 24-O 23-S 26-N 32-C 7 18 8 > 1 > Torsion 25-O 23-S 26-N 27-C 7 18 8 > 1 > Torsion 25-O 23-S 26-N 32-C 7 18 8 > 1 > Torsion 23-S 26-N 27-C 28-C 18 8 1 > 1 > Torsion 23-S 26-N 27-C 50-H 18 8 1 > 5 > Torsion 23-S 26-N 27-C 51-H 18 8 1 > 5 > Torsion 23-S 26-N 32-C 31-C 18 8 1 > 1 > Torsion 23-S 26-N 32-C 60-H 18 8 1 > 5 > Torsion 23-S 26-N 32-C 61-H 18 8 1 > 5 > > MECHANIC -- Some Required Potential Energy Parameters are Undefined > > TINKER is Unable to Continue; Terminating the Current Calculation > > > Thank you, > Divya > --=_75sv1wgpgsb3 Content-Type: text/html; charset=UTF-8 Content-Description: =?utf-8?b?VmVyc2nDs24=?= HTML del mensaje Content-Disposition: inline Content-Transfer-Encoding: 7bit It is most likely because you have atoms in your input file that are not recognised
by the parameter/force field you selected.

This may be due to differences in force field atom naming conventions. Identify the
atoms that give you the trouble and fix their names.

A second possibility is that your geometry is plainly wrong, and thus tinker complains
that it does not correspond to what is coherent with the atomic paramters it has. It might
be because you are using the wrong units and it build a wrong connectivity or because you
actually introduced a weird geometry.

Quoting "divya neelagiri divya.neelagiri0*o*gmail.com":

> Respected sir/madam,
>
>                I am currently working on a project for which I need to use
> tinker. When I tried to find general confirmational analysis for small
> molecules I got this error. I tried all the parameter files. I understood
> that I have some missing parameters but I dont understand how I can get
> them or where I can get them from. Any help in this matter would be great.
> I also sent an attachment which has entire execution. Please reply back
> with some solution. And can you please tell me how I can install FFE for
> GUI for tinker.
>
>
> MECHANIC  --  Some Required Potential Energy Parameters are Undefined
>
>  TINKER is Unable to Continue; Terminating the Current Calculation
>
>
>
>
> This is the complete error message.
>
>
>
>
>
> [divya%%dvs04 outputs_mol2_sdf]$ scan
>
> 
> ##############################################################################
> 
> ##############################################################################
>  ##
> ##
>  ##             TINKER  ---  Software Tools for Molecular
> Design             ##
>  ##
> ##
>  ##                        Version 5.1  February
> 2010                        ##
>  ##
> ##
>  ##               Copyright (c)  Jay William Ponder
> 1990-2010               ##
>  ##                            All Rights
> Reserved                           ##
>  ##
> ##
> 
> ##############################################################################
> 
> ##############################################################################
>
>
>  Enter Cartesian Coordinate File Name :  alkane.xyz
>
>  Enter Potential Parameter File Name :  /data2/pgm/tinker/params/mm2.prm
>
>  Selection of Torsional Angles for Rotation :
>
>     0  - Automatic Selection of Torsional Angles
>     1  - Manual Selection of Angles to Rotate
>     2  - Manual Selection of Angles to Freeze
>
>  Enter the Method of Choice [0] :  0
>
>  Number of Torsions Used in Derivative Computation :    38
>
>  Enter the Number Search Directions for Local Search [5] :  5
>
>  Enter the Energy Threshold for Local Minima [100.0] :  100
>
>  Enter RMS Gradient per Atom Criterion [0.0001] :  0.0001
>
>  Generating Seed Point for Potential Energy Surface Scan
>
>
>     Potential Surface Map       Minimum      1               24.4783
>
>
>  Normal Mode Local Search       Minimum      1
>
> forrtl: error (69): process interrupted (SIGINT)
> Image              PC        Routine            Line
> Source
> scan               080A2A82  Unknown               Unknown  Unknown
> scan               080A1832  Unknown               Unknown  Unknown
> scan               080A039B  Unknown               Unknown  Unknown
> scan               0804A025  Unknown               Unknown  Unknown
> scan               080492D5  Unknown               Unknown  Unknown
> scan               08048261  Unknown               Unknown  Unknown
> scan               0828D8F8  Unknown               Unknown  Unknown
> scan               08048131  Unknown               Unknown  Unknown
> [divya%%dvs04 outputs_mol2_sdf]$ scan
>
> 
> ##############################################################################
> 
> ##############################################################################
>  ##
> ##
>  ##             TINKER  ---  Software Tools for Molecular
> Design             ##
>  ##
> ##
>  ##                        Version 5.1  February
> 2010                        ##
>  ##
> ##
>  ##               Copyright (c)  Jay William Ponder
> 1990-2010               ##
>  ##                            All Rights
> Reserved                           ##
>  ##
> ##
> 
> ##############################################################################
> 
> ##############################################################################
>
>
>  Enter Cartesian Coordinate File Name :  test1.txyz
>
>  Enter Potential Parameter File Name :  /data2/pgm/tinker/params/mm2.prm
>
>  Atoms with an Unusual Number of Attached Atoms :
>
>  Type           Atom Name      Atom Type       Expected    Found
>
>  Valence           8-N              9              3         2
>  Valence          10-O              7              1         2
>  Valence          11-N              9              3         2
>  Valence          20-O              6              4         2
>  Valence          26-N              8              4         3
>
>  Undefined Bond Stretching Parameters :
>
>  Type             Atom Names           Atom Classes
>
>  Bond            3-C      23-S             2   18
>  Bond            9-C      10-O             2    7
>  Bond           10-O      11-N             7    9
>  Bond           12-C      13-O             2    7
>  Bond           14-N      37-H             9    5
>  Bond           17-N      62-H             8    5
>  Bond           23-S      26-N            18    8
>
>  Undefined Angle Bending Parameters :
>
>  Type                  Atom Names                   Atom Classes
>
>  Angle           2-C       3-C      23-S             2    2   18
>  Angle           4-C       3-C      23-S             2    2   18
>  Angle           8-N       9-C      10-O             9    2    7
>  Angle          10-O       9-C      12-C             7    2    2
>  Angle           9-C      10-O      11-N             2    7    9
>  Angle           7-C      11-N      10-O             2    9    7
>  Angle           9-C      12-C      13-O             2    2    7
>  Angle          13-O      12-C      14-N             7    2    9
>  Angle          12-C      14-N      37-H             2    9    5
>  Angle          15-C      14-N      37-H             1    9    5
>  Angle          16-C      17-N      62-H             1    8    5
>  Angle          18-C      17-N      62-H             1    8    5
>  Angle          22-C      17-N      62-H             1    8    5
>  Angle           3-C      23-S      24-O             2   18    7
>  Angle           3-C      23-S      25-O             2   18    7
>  Angle           3-C      23-S      26-N             2   18    8
>  Angle          24-O      23-S      26-N             7   18    8
>  Angle          25-O      23-S      26-N             7   18    8
>  Angle          23-S      26-N      27-C            18    8    1
>  Angle          23-S      26-N      32-C            18    8    1
>
>  Undefined Out-of-Plane Bend Parameters :
>
>  Type                        Atom Names                        Atom Classes
>
>  Angle-OP       23-S       3-C       2-C       4-C          18    2    2
> 2
>  Angle-OP       37-H      14-N      12-C      15-C           5    9    2
> 1
>
>  Undefined Torsional Parameters :
>
>  Type                        Atom Names                        Atom Classes
>
>  Torsion         1-C       2-C       3-C      23-S           2    2    2
> 18
>  Torsion        34-H       2-C       3-C      23-S           5    2    2
> 18
>  Torsion        23-S       3-C       4-C       5-C          18    2    2
> 2
>  Torsion        23-S       3-C       4-C      35-H          18    2    2
> 5
>  Torsion         2-C       3-C      23-S      24-O           2    2   18
> 7
>  Torsion         2-C       3-C      23-S      25-O           2    2   18
> 7
>  Torsion         2-C       3-C      23-S      26-N           2    2   18
> 8
>  Torsion         4-C       3-C      23-S      24-O           2    2   18
> 7
>  Torsion         4-C       3-C      23-S      25-O           2    2   18
> 7
>  Torsion         4-C       3-C      23-S      26-N           2    2   18
> 8
>  Torsion        11-N       7-C       8-N       9-C           9    2    9
> 2
>  Torsion         6-C       7-C      11-N      10-O           2    2    9
> 7
>  Torsion         8-N       7-C      11-N      10-O           9    2    9
> 7
>  Torsion         7-C       8-N       9-C      10-O           2    9    2
> 7
>  Torsion         8-N       9-C      10-O      11-N           9    2    7
> 9
>  Torsion        12-C       9-C      10-O      11-N           2    2    7
> 9
>  Torsion         8-N       9-C      12-C      13-O           9    2    2
> 7
>  Torsion         8-N       9-C      12-C      14-N           9    2    2
> 9
>  Torsion        10-O       9-C      12-C      13-O           7    2    2
> 7
>  Torsion        10-O       9-C      12-C      14-N           7    2    2
> 9
>  Torsion         9-C      10-O      11-N       7-C           2    7    9
> 2
>  Torsion         9-C      12-C      14-N      37-H           2    2    9
> 5
>  Torsion        13-O      12-C      14-N      15-C           7    2    9
> 1
>  Torsion        13-O      12-C      14-N      37-H           7    2    9
> 5
>  Torsion        37-H      14-N      15-C      16-C           5    9    1
> 1
>  Torsion        37-H      14-N      15-C      38-H           5    9    1
> 5
>  Torsion        37-H      14-N      15-C      39-H           5    9    1
> 5
>  Torsion        15-C      16-C      17-N      62-H           1    1    8
> 5
>  Torsion        40-H      16-C      17-N      62-H           5    1    8
> 5
>  Torsion        41-H      16-C      17-N      62-H           5    1    8
> 5
>  Torsion        62-H      17-N      18-C      19-C           5    8    1
> 1
>  Torsion        62-H      17-N      18-C      42-H           5    8    1
> 5
>  Torsion        62-H      17-N      18-C      43-H           5    8    1
> 5
>  Torsion        62-H      17-N      22-C      21-C           5    8    1
> 1
>  Torsion        62-H      17-N      22-C      48-H           5    8    1
> 5
>  Torsion        62-H      17-N      22-C      49-H           5    8    1
> 5
>  Torsion         3-C      23-S      26-N      27-C           2   18    8
> 1
>  Torsion         3-C      23-S      26-N      32-C           2   18    8
> 1
>  Torsion        24-O      23-S      26-N      27-C           7   18    8
> 1
>  Torsion        24-O      23-S      26-N      32-C           7   18    8
> 1
>  Torsion        25-O      23-S      26-N      27-C           7   18    8
> 1
>  Torsion        25-O      23-S      26-N      32-C           7   18    8
> 1
>  Torsion        23-S      26-N      27-C      28-C          18    8    1
> 1
>  Torsion        23-S      26-N      27-C      50-H          18    8    1
> 5
>  Torsion        23-S      26-N      27-C      51-H          18    8    1
> 5
>  Torsion        23-S      26-N      32-C      31-C          18    8    1
> 1
>  Torsion        23-S      26-N      32-C      60-H          18    8    1
> 5
>  Torsion        23-S      26-N      32-C      61-H          18    8    1
> 5
>
>  MECHANIC  --  Some Required Potential Energy Parameters are Undefined
>
>  TINKER is Unable to Continue; Terminating the Current Calculation
>
>
> Thank you,
> Divya
>
--=_75sv1wgpgsb3-- From owner-chemistry@ccl.net Wed Nov 16 12:54:00 2011 From: "Isabelle Navizet isabelle.navizet]~[wits.ac.za" To: CCL Subject: CCL: tinker Message-Id: <-45889-111116092008-14998-gJ86XGl4Y+BYEU28mnDFiA[a]server.ccl.net> X-Original-From: Isabelle Navizet Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="UTF-8" Date: Wed, 16 Nov 2011 16:19:19 +0200 Mime-Version: 1.0 Sent to CCL by: Isabelle Navizet [isabelle.navizet++wits.ac.za] Hello Divya, At a first glance, you did not put the correct parameters for some of the atoms in the .xyz file. For exemple : > Type Atom Name Atom Type Expected Found > Valence 8-N 9 3 2 means that the 8th atom N has an atom type 9 "NSP2 AMIDE" so should have 3 neighbor atoms bonded to it but in your .xyz only 2 atoms are connected to this N. This means that the atom type is wrong or the connectivity is wrong in your .xyz Hope this help Isabelle -- Dr Isabelle Navizet School of Chemistry, Humphrey Raikes Building, room 105 University of the Witwatersrand, Johannesburg Private Bag 3, PO Wits, South Africa New Tel +27+11+7176704 Fax +27+11+7176749

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From owner-chemistry@ccl.net Wed Nov 16 13:29:00 2011 From: "Roby Kurian Roby_Kurian/a\umit.maine.edu" To: CCL Subject: CCL: ONIOM input Message-Id: <-45890-111116093333-25363-fMM5ZM31vH7bY/eL2tW0qA]_[server.ccl.net> X-Original-From: "Roby Kurian" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 16 Nov 2011 09:33:37 -0500 MIME-Version: 1.0 Sent to CCL by: "Roby Kurian" [Roby_Kurian-$-umit.maine.edu] "CCL Subscribers" writes: > >Sent to CCL by: "Erik D az" [enterdiceck(-)hotmail.com] >Hello! >I have a question about ONIOM inputs... I write this lines (I work with Cisplatin derivates): > >%chk=oniomprueba >%mem=512MB >%nproc=8 ># opt=maxcycle=256 oniom(pbepbe/gen:pbepbe/3-21G) scf=qc geom=connectivity pseudo=read > >oniomprueba > >0 1 0 1 0 1 > >molecule specification > >Pt 0 >SDD >**** >1 3 4 5 6 7 8 9 10 11 0 >6-31G(d,p) >**** >Pt 0 >SDD > > >The message in the output file is the next: > >ONIOM: Cut between C /H 7 and N 1 factor= 0.700189 0.700189 > ONIOM: saving gridpoint 17 > ONIOM: restoring gridpoint 3 on chk file. > ONIOM: generating point 3 -- low level on real system. > Standard basis: 3-21G (6D, 7F) > 3-21G basis sets are only available up to Xe. > Error termination via Lnk1e in /home//g09/l301.exe > >My question is, how i can solve this problem and have a normal termination? The Basis set 3_21G cannot handle heavier atoms like Pt. So you will have to supply external basis set. You can get those from EMSL (https://bse.pnl.gov/bse/portal). You will need to add thata basis set to the end of your current input file. It goes like this. Leave a blank line where the input file ends. List all other atoms other than Pt in your calculation define the basis set you use for those atoms **** Paste the external basis set here. Here is an example. 140 (last line of my input file) C H O N S P (listing all other atoms in the molecule) 6-31g+(d) (defining basis set for those atoms) **** Au 0 (beginning of the LANL2DZ basis set I am using for Gold) S 3 1.00 2.8090000 -1.2021556 1.5950000 1.6741578 0.5327000 0.3526593 Hope it helps. Roby