From owner-chemistry@ccl.net Wed Sep 21 03:43:00 2011 From: "bonoit dahmani bonoit_10||yahoo.fr" To: CCL Subject: CCL:G: Re : CCL:G: Problem in preparing a proper input geometry for ONIOM calculations Message-Id: <-45485-110921033845-13631-0Z7+jbSqWtt9gqWMQqMaaA^-^server.ccl.net> X-Original-From: bonoit dahmani Content-Type: multipart/alternative; boundary="-1506579523-1761622223-1316590693=:61903" Date: Wed, 21 Sep 2011 08:38:13 +0100 (BST) MIME-Version: 1.0 Sent to CCL by: bonoit dahmani [bonoit_10[]yahoo.fr] ---1506579523-1761622223-1316590693=:61903 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Krati, As it's suggested by the programm, you've an internal coordinate system pro= blem. So, i advice you to set a new structure of your systemand try to abstract a= n hydrogen atom=A0from a layer=A0when=A0you select the layers=A0( i mean on= e hydrogen atom will be selected in another layer) Try that, perhaps it works Sincerely Bonoit --- En date de=A0: Lun 19.9.11, krati joshi kjjulie.joshi/./gmail.com a =E9crit=A0: De: krati joshi kjjulie.joshi/./gmail.com Objet: CCL:G: Problem in preparing a proper input geometry for ONIOM calcul= ations =C0: "Bonoir, Bonoir " Date: Lundi 19 septembre 2011, 13h56 Hello sir, =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Thanks for the suggestion. I checke= d the output file but i found that=A0all the values are ok. I am providing = you small portion of my output file=A0=20 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 as follows- =A0 =A0Eigenvalue=A0=A0 256 is=A0=A0 5.23D-07 should be less than=A0=A0=A0=A0 0= .000000 Eigenvector: =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 D3= 195=A0=A0=A0=A0 D1317=A0=A0=A0=A0 D1333=A0=A0=A0=A0 D1325=A0=A0=A0=A0 D1337 =A0=A0 1=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.48429= =A0=A0 0.36738=A0 -0.30987=A0 -0.29524=A0 -0.29485 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 D3= 203=A0=A0=A0=A0 D1321=A0=A0=A0=A0 D3207=A0=A0=A0=A0 D3197=A0=A0=A0=A0=A0 R1= 1 =A0=A0 1=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 -0.27254=A0= =A0 0.26387=A0 -0.20482=A0 -0.19972=A0 -0.16424 =A0Eigenvalue=A0=A0 257 is=A0=A0 4.63D-07 should be less than=A0=A0=A0=A0 0= .000000 Eigenvector: =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 D1= 325=A0=A0=A0=A0 D3199=A0=A0=A0=A0 D1329=A0=A0=A0=A0 D3201=A0=A0=A0=A0 D3207 =A0=A0 1=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.53407= =A0=A0 0.39381=A0 -0.37243=A0 -0.36063=A0 -0.30389 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 D1= 337=A0=A0=A0=A0 D1333=A0=A0=A0=A0=A0 R11=A0=A0=A0=A0=A0 D3195=A0=A0=A0=A0 D= 3203 =A0=A0 1=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 -0.23305=A0 = -0.18893=A0 -0.14606=A0=A0 0.10917=A0 -0.09532 =A0Eigenvalue=A0=A0 258 is=A0=A0 4.06D-07 should be less than=A0=A0=A0=A0 0= .000000 Eigenvector: =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 D1= 333=A0=A0=A0=A0 D1329=A0=A0=A0=A0 D1317=A0=A0=A0=A0 D1325=A0=A0=A0=A0 D3199 =A0=A0 1=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.60892= =A0 -0.34587=A0=A0 0.31007=A0 -0.29786=A0=A0 0.22521 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 D3= 203=A0=A0=A0=A0 D1321=A0=A0=A0=A0=A0 R11=A0=A0=A0=A0=A0=A0 R6=A0=A0=A0=A0= =A0=A0 D3207 =A0=A0 1=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 -0.21351=A0 = -0.20886=A0 -0.18784=A0 -0.15529=A0 -0.15423 =A0Eigenvalue=A0=A0 259 is=A0=A0 2.81D-07 should be less than=A0=A0=A0=A0 0= .000000 Eigenvector: =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 D1= 329=A0=A0=A0=A0 D3197=A0=A0=A0=A0 D3203=A0=A0=A0=A0 D3205=A0=A0=A0=A0=A0 R1= 6 =A0=A0 1=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.35545= =A0=A0 0.34698=A0 -0.30807=A0=A0 0.30120=A0 -0.26150 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 D1= 317=A0=A0=A0=A0 D3201=A0=A0=A0=A0=A0 R17=A0=A0=A0=A0=A0 D1325=A0=A0=A0=A0= =A0 R4 =A0=A0 1=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 -0.21696=A0 = -0.21311=A0 -0.21273=A0 -0.19237=A0 -0.18615 =A0Eigenvalue=A0=A0 260 is=A0=A0 2.31D-07 should be less than=A0=A0=A0=A0 0= .000000 Eigenvector: =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 D1= 341=A0=A0=A0=A0 D1321=A0=A0=A0=A0 D1325=A0=A0=A0=A0 D3205=A0=A0=A0=A0 D1317 =A0=A0 1=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.45403= =A0=A0 0.42095=A0 -0.30288=A0 -0.28021=A0 -0.27618 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 D1= 329=A0=A0=A0=A0 D3199=A0=A0=A0=A0=A0 R11=A0=A0=A0=A0=A0 D3207=A0=A0=A0=A0= =A0 R6 =A0=A0 1=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 -0.26705=A0= =A0 0.24524=A0=A0 0.20178=A0 -0.16533=A0=A0 0.16409 =A0Eigenvalue=A0=A0 261 is=A0=A0 1.79D-07 should be less than=A0=A0=A0=A0 0= .000000 Eigenvector: =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= R16=A0=A0=A0=A0=A0=A0 R17=A0=A0=A0=A0=A0=A0 R13=A0=A0=A0=A0=A0=A0 R12=A0= =A0=A0=A0=A0 D3199 =A0=A0 1=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.43305= =A0=A0 0.39082=A0=A0 0.25109=A0 -0.23849=A0=A0 0.21929 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= R11=A0=A0=A0=A0=A0=A0 R4=A0=A0=A0=A0=A0=A0 D1337=A0=A0=A0=A0 D1317=A0=A0= =A0=A0 D3201 =A0=A0 1=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 -0.18287=A0= =A0 0.17637=A0=A0 0.17231=A0 -0.16282=A0 -0.15542 =A0Eigenvalue=A0=A0 262 is=A0=A0 1.53D-07 should be less than=A0=A0=A0=A0 0= .000000 Eigenvector: =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= R11=A0=A0=A0=A0=A0=A0 R4=A0=A0=A0=A0=A0=A0 D3201=A0=A0=A0=A0 D1317=A0=A0= =A0=A0=A0 R7 =A0=A0 1=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.72761= =A0=A0 0.28931=A0 -0.19429=A0=A0 0.16647=A0=A0 0.14439 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 D3= 203=A0=A0=A0=A0 D1341=A0=A0=A0=A0 D3207=A0=A0=A0=A0=A0 R13=A0=A0=A0=A0=A0 D= 3205 =A0=A0 1=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 -0.14225=A0 = -0.13633=A0 -0.13097=A0=A0 0.12776=A0=A0 0.12450 =A0Eigenvalue=A0=A0 263 is=A0=A0 1.07D-07 should be less than=A0=A0=A0=A0 0= .000000 Eigenvector: =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= R13=A0=A0=A0=A0=A0=A0 R6=A0=A0=A0=A0=A0=A0=A0 R17=A0=A0=A0=A0=A0=A0 R8=A0= =A0=A0=A0=A0=A0=A0 R22 =A0=A0 1=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.50511= =A0 -0.49306=A0 -0.28162=A0=A0 0.19005=A0 -0.16163 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= R24=A0=A0=A0=A0=A0=A0 R14=A0=A0=A0=A0=A0=A0 R27=A0=A0=A0=A0=A0=A0 R18=A0= =A0=A0=A0=A0 D1321 =A0=A0 1=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.15881= =A0 -0.15067=A0=A0 0.14746=A0 -0.13866=A0=A0 0.13633 =A0NTrRot=3D=A0 4233 NTRed=3D=A0 4479 NAtoms=3D=A0=A0=A0 84 NSkip=3D=A0 423= 3 IsLin=3DF =A0Error in internal coordinate system. =A0Error termination via Lnk1e in /home/raj/gaussian09//g09/l103.exe at Sun= Sep 18 03:24:21 2011. =A0Job cpu time:=A0 0 days=A0 8 hours 41 minutes 38.2 seconds. =A0File lengths (MBytes):=A0 RWF=3D=A0=A0=A0 818 Int=3D=A0=A0=A0=A0=A0 0 D2= E=3D=A0=A0=A0=A0=A0 0 Chk=3D=A0=A0=A0 270 Scr=3D=A0=A0=A0=A0=A0 1 =A0 =A0My input file looks like- =A0=20 %mem=3D2500MB %chk=3DQ025-ONICAL2-70.chk #p opt oniom(b3lyp/dgdzvp:uff) nosymm geom=3Dconnect Q025-cal2-70 0 1 0 1 0 1 Si-Si3 0 -0.36206632 0.54077205 -0.51931236 H O-O_2 0 1.19460468 0.78686805 -0.06577136 H O-O_2 0 -1.20290432 0.77435105 0.88184164 H O-O_2 0 -0.44703432 -1.04638495 -0.95862036 H O-O_2 0 -0.84419432 1.59445505 -1.69660236 H =A0 If u have some time=A0pls look into the matter and=A0 give me some suggesti= ons pls.Thanks in advance. =A0 =A0 Krati Joshi NCL Pune =A0 =A0 =A0 =A0 =A0 ---1506579523-1761622223-1316590693=:61903 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable ---1506579523-1761622223-1316590693=:61903-- From owner-chemistry@ccl.net Wed Sep 21 08:25:00 2011 From: "Andrew Dalke dalke * dalkescientific.com" To: CCL Subject: CCL: ANN: chemfp-1.0 Message-Id: <-45486-110920183515-15750-gkCD8xIVKvdJSKsjwoJJqQ_._server.ccl.net> X-Original-From: Andrew Dalke Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Tue, 20 Sep 2011 23:36:30 +0100 Mime-Version: 1.0 (Apple Message framework v1084) Sent to CCL by: Andrew Dalke [dalke*o*dalkescientific.com] I've just released version 1.0 of my chemfp project. chemfp is a free set of command-line tools, and the underlying Python software library, for generating cheminformatics fingerprint files and searching them based on Tanimoto similarity. It can use the Open Babel, OEChem, or RDKit chemistry toolkits to convert structure files into fingerprint files. It also has a tool to extract fingerprints from fields in an SD file, including special support for PubChem's CACTVS substructure field. The similarity search program does fast Tanimoto searches of a set of queries against a set of targets, with a user-defined minimum threshold score and/or a k-nearest neighbors option. For more information, follow these links: Project home page: http://code.google.com/p/chem-fingerprints/ Documentation: http://readthedocs.org/docs/chemfp/en/latest/ Direct download: http://chem-fingerprints.googlecode.com/files/chemfp-1.0.tar.gz Let me know if you find it useful, or if there are any problems. Andrew Dalke dalke!A!dalkescientific.com Advertisement: I develop custom chemistry software and do Python training for scientists. Are you interested in hiring my services? If you're in Ireland or England it might even be easy to meet! I'm visiting the Dublin area until 8 October, then two weeks near Oxford and Cambridge. From owner-chemistry@ccl.net Wed Sep 21 09:09:00 2011 From: "VS Kumar N nvskumar123^_^gmail.com" To: CCL Subject: CCL:G: error in microsolvation calculation Message-Id: <-45487-110921090634-13476-R3SR1loLC/BjGCJHSoqCXw:-:server.ccl.net> X-Original-From: "VS Kumar N" Date: Wed, 21 Sep 2011 09:06:31 -0400 Sent to CCL by: "VS Kumar N" [nvskumar123|a|gmail.com] Dear CCL members, The following shows how a Gaussian job on microsolvation calculations on a peptide molecule got error termination. Item Value Threshold Converged? Maximum Force 0.005165 0.000450 NO RMS Force 0.000361 0.000300 NO Maximum Displacement NaN 0.001800 YES RMS Displacement NaN 0.001200 YES Predicted change in Energy= NaN GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Small interatomic distances encountered: 2 1 3 1 3 2 4 1 ... ... Problem with the distance matrix. Error termination via Lnk1e in /sw/g03/l202.exe at Sat Sep 17 01:37:32 2011. Job cpu time: 1 days 19 hours 28 minutes 44.7 seconds. File lengths (MBytes): RWF= 460 Int= 0 D2E= 0 Chk= 52 Scr= 1 The out put geometry looks normal with respect to distances. What is meaning numbers given below 'Small interatomic distances ...' and also please suggest what kind changes I have to made in the input file. kumar From owner-chemistry@ccl.net Wed Sep 21 10:18:00 2011 From: "Wolf Ihlenfeldt wdi-#-xemistry.com" To: CCL Subject: CCL: ANN: chemfp-1.0 Message-Id: <-45488-110921100748-24065-Zth+j6hYDj9Szpw3PNEBUw{}server.ccl.net> X-Original-From: Wolf Ihlenfeldt Content-Type: multipart/alternative; boundary=0016364996dbcdd62b04ad74181f Date: Wed, 21 Sep 2011 16:07:30 +0200 MIME-Version: 1.0 Sent to CCL by: Wolf Ihlenfeldt [wdi-*-xemistry.com] --0016364996dbcdd62b04ad74181f Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable An additional note: Since version 3.188, the Cactvs toolkit (www.xemistry.com/academic for free academic/educational downloads) comes with an I/O module for the FPS format, and can both read and write it. The toolkit has support for various fingerprint algorithms, and also supports the PubChem fingerprint encoding in SD-files as well as the native PubChem ASN.1 binary and text formats. On Wed, Sep 21, 2011 at 12:36 AM, Andrew Dalke dalke * dalkescientific.com = < owner-chemistry],[ccl.net> wrote: > > Sent to CCL by: Andrew Dalke [dalke*o*dalkescientific.com] > I've just released version 1.0 of my chemfp project. > > chemfp is a free set of command-line tools, and the underlying Python > software library, for generating cheminformatics fingerprint files > and searching them based on Tanimoto similarity. > > It can use the Open Babel, OEChem, or RDKit chemistry toolkits > to convert structure files into fingerprint files. It also has > a tool to extract fingerprints from fields in an SD file, including > special support for PubChem's CACTVS substructure field. > > The similarity search program does fast Tanimoto searches of > a set of queries against a set of targets, with a user-defined > minimum threshold score and/or a k-nearest neighbors option. > > For more information, follow these links: > > Project home page: http://code.google.com/p/chem-fingerprints/ > Documentation: http://readthedocs.org/docs/chemfp/en/latest/ > Direct download: > http://chem-fingerprints.googlecode.com/files/chemfp-1.0.tar.gz > > Let me know if you find it useful, or if there are any problems. > > Andrew Dalke > dalke+*+dalkescientific.com > > Advertisement: > I develop custom chemistry software and do Python training for > scientists. Are you interested in hiring my services? If you're in > Ireland or England it might even be easy to meet! I'm visiting the > Dublin area until 8 October, then two weeks near Oxford and Cambridge. > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 Wolf-D. Ihlenfeldt - Xemistry GmbH - wdi],[xemistry.com Phone: +49 6174 201455 - Fax +49 6174 209665 --- xemistry gmbh =E2=80=93 Gesch=C3=A4ftsf=C3=BChrer/Managing Director: Dr. W.= D. Ihlenfeldt Address: Hainholzweg 11, D-61462 K=C3=B6nigstein, Germany HR K=C3=B6nigstein B7522 : Ust/VAT ID DE215316329 : DUNS 34-400-1719 --0016364996dbcdd62b04ad74181f Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
An additional note:

Since version 3.188, the Cactvs toolkit (www.xemistry.com/academic for= free academic/educational downloads) comes with=C2=A0 an I/O module for th= e FPS format, and can both read and write it. The toolkit has support for v= arious fingerprint algorithms, and also supports=C2=A0 the PubChem fingerpr= int encoding in SD-files as well as the native PubChem ASN.1 binary and tex= t formats.

On Wed, Sep 21, 2011 at 12:36 AM, Andrew Dal= ke dalke * dalkescientific.com <= span dir=3D"ltr"><owner-chemi= stry],[ccl.net> wrote:

Sent to CCL by: Andrew Dalke [dalke*o*dalkescientific.com]
I've just released version 1.0 of my chemfp project.

chemfp is a free set of command-line tools, and the underlying Python
software library, for generating cheminformatics fingerprint files
and searching them based on Tanimoto similarity.

It can use the Open Babel, OEChem, or RDKit chemistry toolkits
to convert structure files into fingerprint files. It also has
a tool to extract fingerprints from fields in an SD file, including
special support for PubChem's CACTVS substructure field.

The similarity search program does fast Tanimoto searches of
a set of queries against a set of targets, with a user-defined
minimum threshold score and/or a k-nearest neighbors option.

For more information, follow these links:

=C2=A0Project home page: http://code.google.com/p/chem-fingerprints/ =C2=A0Documentation: http://readthedocs.org/docs/chemfp/en/latest/ =C2=A0Direct download: http://chem-fingerprints.googlec= ode.com/files/chemfp-1.0.tar.gz

Let me know if you find it useful, or if there are any problems.

=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0Andrew Dalke
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0dalke+*+dalkescientific.com

Advertisement:
=C2=A0I develop custom chemistry software and do Python training for
scientists. Are you interested in hiring my services? If you're in
Ireland or England it might even be easy to meet! I'm visiting the
Dublin area until 8 October, then two weeks near Oxford and Cambridge.



-=3D This is automatically added to each message by the mailing script =3D-=
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--0016364996dbcdd62b04ad74181f-- From owner-chemistry@ccl.net Wed Sep 21 10:52:01 2011 From: "Morad El-Hendawy m80elhendawy%yahoo.com" To: CCL Subject: CCL:G: error in microsolvation calculation Message-Id: <-45489-110921104105-11819-CXsmfGHwDXDZlOVBfyXXXg],[server.ccl.net> X-Original-From: Morad El-Hendawy Content-Type: multipart/alternative; boundary="9991677-557433333-1316616008=:56911" Date: Wed, 21 Sep 2011 07:40:08 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Morad El-Hendawy [m80elhendawy*yahoo.com] --9991677-557433333-1316616008=:56911 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Kumar,=0A=0AThe problem you have obtained can be solved by=A0 restarti= ng optimization from a different input geometry. =0A=0AThe small interatomi= c distances encountered:=0A=A0 =A0 2=A0 =A0 1=0A=0A=A0 =A0 3=A0 =A0 1=0A= =0A=A0 =A0 3=A0 =A0 2=0A=0A=A0 =A0 4=A0 =A0 1=0A=0AFor example 2 1 mean t= he distance between atom #2 and atom #1 is small.=0A=0AYou can draw the str= ucture by GaussView and then press CLEAN icons to get a better intial geome= try. If you have not a GaussView =0A=0A=0AHope this help,=0A=0AMorad M. El-= Hendawy=0A=0A=0A________________________________=0AFrom: VS Kumar N nvskuma= r123^_^gmail.com =0ATo: "El-Hendawy, Morad Metwall= y " =0ASent: Wednesday, September 21, 2011 = 2:06 PM=0ASubject: CCL:G: error in microsolvation calculation=0A=0A=0ASent = to CCL by: "VS Kumar N" [nvskumar123|a|gmail.com]=0ADear CCL members,=0A=0A= The following shows how a Gaussian job on microsolvation calculations on a = peptide molecule got error termination. =0A=0A=0A=A0 =A0 =A0 =A0 Item=A0 = =A0 =A0 =A0 =A0 =A0 =A0 Value=A0 =A0 Threshold=A0 Converged?=0AMaximum Fo= rce=A0 =A0 =A0 =A0 =A0 =A0 0.005165=A0 =A0 0.000450=A0 =A0 NO=0ARMS=A0 = =A0 Force=A0 =A0 =A0 =A0 =A0 =A0 0.000361=A0 =A0 0.000300=A0 =A0 NO=0AMa= ximum Displacement=A0 =A0 =A0 =A0 =A0 NaN=A0 =A0 0.001800=A0 =A0 YES=0ARM= S=A0 =A0 Displacement=A0 =A0 =A0 =A0 =A0 NaN=A0 =A0 0.001200=A0 =A0 YES= =0APredicted change in Energy=3D=A0 =A0 =A0 =A0 =A0 NaN=0AGradGradGradGradG= radGradGradGradGradGradGradGradGradGradGradGradGradGrad=0A=0ASmall interato= mic distances encountered:=0A=A0 =A0 2=A0 =A0 1=0A=0A=A0 =A0 3=A0 =A0 1= =0A=0A=A0 =A0 3=A0 =A0 2=0A=0A=A0 =A0 4=A0 =A0 1=0A...=0A...=0A=0AProblem= with the distance matrix.=0AError termination via Lnk1e in /sw/g03/l202.ex= e at Sat Sep 17 01:37:32 2011.=0AJob cpu time:=A0 1 days 19 hours 28 minute= s 44.7 seconds.=0AFile lengths (MBytes):=A0 RWF=3D=A0 =A0 460 Int=3D=A0 =A0= =A0 0 D2E=3D=A0 =A0 =A0 0 Chk=3D=A0 =A0 52 Scr=3D=A0 =A0 =A0 1=0A=0A=0ATh= e out put geometry looks normal with respect to distances. What is meaning = numbers given below 'Small interatomic distances ...' and also please sugge= st what kind changes I have to made in the input file. =0A=0Akumar=0A=0A=0A= =0A-=3D This is automatically added to each message by the mailing script = =3D-=0ATo recover the email address of the author of the message, please ch= ange=0A= =0A=0A=0AE-mail to sub= scribers: CHEMISTRY * ccl.net or use:=0A=A0 =A0 =A0 http://www.ccl.net/cgi-bi= n/ccl/send_ccl_message=0A=0AE-mail to administrators: CHEMISTRY-REQUEST * ccl= .net or use=0A=A0 =A0 =A0= =0A=0A=0A=A0 =A0 =A0 http://www.ccl.net/chemistry/su= b_unsub.shtml=0A=0A= =0A=0A=0AConferences: http://server.ccl.net/ch= emistry/announcements/conferences/=0A=0ASearch Messages: http://www.ccl.net= /chemistry/searchccl/index.shtml=0A=0AIf your mail bounces from CCL with 5.= 7.1 error, check:=0A=A0 =A0 =A0=0A=0ARTFI: = http://www.ccl.net/chemistry/aboutccl/instructions/ --9991677-557433333-1316616008=:56911 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Kumar= ,

The problem you have o= btained can be solved by  restarting optimization from a differ= ent input geometry.
=
The small interatomic distances encountered:
    2 =   1

    3    1

    3&nb= sp;   2

    4    1

For example 2 1 mean the distance between atom #2 and atom #1 is small.

You can draw the structure by GaussView and then p= ress CLEAN icons to get a better intial geometry. If you have not a GaussVi= ew

Hope this help,

M= orad M. El-Hendawy

F= rom: VS Kumar N nvskumar123^_^gmail.com <owner-chemistry * ccl.= net>
To: "El-Hendawy= , Morad Metwally " <m80elhendawy * yahoo.com>
Sent: Wednesday, September 21, 2011 2:06= PM
Subject: CCL:G: err= or in microsolvation calculation


Sent to CCL by: "VS Kuma= r N" [nvskumar123|a|gmail.com]
Dear CCL members,

The following s= hows how a Gaussian job on microsolvation calculations on a peptide molecul= e got error termination.


        Item =             Value    Threshold&n= bsp; Converged?
Maximum Force            0.00= 5165    0.000450    NO
RMS    Force&nb= sp;           0.000361    0.000300 = ;   NO
Maximum Displacement          NaN=     0.001800    YES
RMS    Displacemen= t          NaN    0.001200   = YES
Predicted change in Energy=3D          N= aN
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad= Grad

Small interatomic distances encountered:
    2&n= bsp;   1

    3    1

    = 3    2

    4    1
...
...
Problem with the distance matrix.
Error termination via Lnk1e in /sw/= g03/l202.exe at Sat Sep 17 01:37:32 2011.
Job cpu time:  1 days 19 hours 28 minutes 44.7 seconds.
File lengths (MBytes):  RW= F=3D    460 Int=3D      0 D2E=3D    &nbs= p; 0 Chk=3D    52 Scr=3D      1


The ou= t put geometry looks normal with respect to distances. What is meaning numb= ers given below 'Small interatomic distances ...' and also please suggest w= hat kind changes I have to made in the input file.

kumar


-=3D This is automatically added to each message by the mailing script= =3D-
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--9991677-557433333-1316616008=:56911-- From owner-chemistry@ccl.net Wed Sep 21 11:28:01 2011 From: "Victor Rosas Garcia rosas.victor]=[gmail.com" To: CCL Subject: CCL: GAMESS queries Message-Id: <-45490-110921104106-11848-o0CEAy2tFhwOp781szC+gw=server.ccl.net> X-Original-From: Victor Rosas Garcia Content-Type: multipart/alternative; boundary=000e0cd3401231bd7e04ad7490c8 Date: Wed, 21 Sep 2011 09:40:53 -0500 MIME-Version: 1.0 Sent to CCL by: Victor Rosas Garcia [rosas.victor^gmail.com] --000e0cd3401231bd7e04ad7490c8 Content-Type: text/plain; charset=ISO-8859-1 Hi Liz, This error message could mean that either the basis set or the element was not found in the external basis file. Which element is "^|^|" ? Hope this helps. Victor 2011/9/20 Liz L eli_lsh]![yahoo.com.hk > > Sent to CCL by: "Liz L" [eli_lsh(0)yahoo.com.hk] > Hi all, > > I'm following the instructions in http://www.somewhereville.com/?p=24 > for establishing external basis set file in running GAMESS. However, I > kept getting the error message: > *** ELEMENT "^|^|" BASIS "MIXEDBAS" WAS NOT FOUND IN THE EXTERNAL BASIS > FILE *** > even though I've double checked with the EXTFILE.txt and use $BASIS > EXTFIL=.TRUE. GBASIS=MIXEDBAS > $END in the input file. > > Please if anyone can advise? > Thanks so much! > Liz> > > --000e0cd3401231bd7e04ad7490c8 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Liz,

This error message could mean that either the basis set or t= he element was not found in the external basis file.

Which element i= s "^|^|" ?

Hope this helps.

Victor

2011/9/20 Liz L eli_lsh]![yahoo.com.hk = <owner-chem= istry.=.ccl.net>

Sent to CCL by: "Liz =A0L" [eli_lsh(0)yahoo.com.hk]
Hi all,

I'm following the instructions in http://www.somewhereville.com/?p=3D24 for establishing external basis set file in running GAMESS. =A0However, I k= ept getting the error message:
=A0*** ELEMENT "^|^|" BASIS "MIXEDBAS" WAS NOT FOUND IN= THE EXTERNAL BASIS FILE ***
even though I've double checked with the EXTFILE.txt and use $BASIS EXT= FIL=3D.TRUE. GBASIS=3DMIXEDBAS
$END in the input file.

Please if anyone can advise?
Thanks so much!
Liz



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--000e0cd3401231bd7e04ad7490c8-- From owner-chemistry@ccl.net Wed Sep 21 14:47:01 2011 From: "Rajarshi Guha rajarshi.guha-$-gmail.com" To: CCL Subject: CCL: ANN: chemfp-1.0 Message-Id: <-45491-110921112516-24487-JSIENBhnwSwxnF88kg2VOQ*server.ccl.net> X-Original-From: Rajarshi Guha Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252 Date: Wed, 21 Sep 2011 11:25:06 -0400 MIME-Version: 1.0 Sent to CCL by: Rajarshi Guha [rajarshi.guha===gmail.com] In a similar spirit, the FPS format is also supported in R via the fingerprint package (http://cran.r-project.org/web/packages/fingerprint/index.html) On Wed, Sep 21, 2011 at 10:07 AM, Wolf Ihlenfeldt wdi-#-xemistry.com wrote: > > An additional note: > > Since version 3.188, the Cactvs toolkit (www.xemistry.com/academic for free > academic/educational downloads) comes with  an I/O module for the FPS > format, and can both read and write it. The toolkit has support for various > fingerprint algorithms, and also supports  the PubChem fingerprint encoding > in SD-files as well as the native PubChem ASN.1 binary and text formats. > > On Wed, Sep 21, 2011 at 12:36 AM, Andrew Dalke dalke * dalkescientific.com > wrote: >> >> Sent to CCL by: Andrew Dalke [dalke*o*dalkescientific.com] >> I've just released version 1.0 of my chemfp project. >> >> chemfp is a free set of command-line tools, and the underlying Python >> software library, for generating cheminformatics fingerprint files >> and searching them based on Tanimoto similarity. >> >> It can use the Open Babel, OEChem, or RDKit chemistry toolkits >> to convert structure files into fingerprint files. It also has >> a tool to extract fingerprints from fields in an SD file, including >> special support for PubChem's CACTVS substructure field. >> >> The similarity search program does fast Tanimoto searches of >> a set of queries against a set of targets, with a user-defined >> minimum threshold score and/or a k-nearest neighbors option. >> >> For more information, follow these links: >> >>  Project home page: http://code.google.com/p/chem-fingerprints/ >>  Documentation: http://readthedocs.org/docs/chemfp/en/latest/ >>  Direct download: >> http://chem-fingerprints.googlecode.com/files/chemfp-1.0.tar.gz >> >> Let me know if you find it useful, or if there are any problems. >> >>                                Andrew Dalke >>                                dalke+*+dalkescientific.com >> >> Advertisement: >>  I develop custom chemistry software and do Python training for >> scientists. Are you interested in hiring my services? If you're in >> Ireland or England it might even be easy to meet! I'm visiting the >> Dublin area until 8 October, then two weeks near Oxford and Cambridge.>> E-mail to subscribers: CHEMISTRY++ccl.net or use: >>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message >> >> E-mail to administrators: CHEMISTRY-REQUEST++ccl.net or use >>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>>      http://www.ccl.net/chemistry/sub_unsub.shtml>>      http://www.ccl.net/spammers.txt>> >> > > > > -- > Wolf-D. Ihlenfeldt -  Xemistry GmbH - wdi++xemistry.com > Phone: +49 6174 201455 - Fax +49 6174 209665 > --- > xemistry gmbh – Geschäftsführer/Managing Director: Dr. W. D. Ihlenfeldt > Address: Hainholzweg 11, D-61462 Königstein, Germany > HR Königstein B7522 : Ust/VAT ID DE215316329 : DUNS 34-400-1719 > > -- Rajarshi Guha NIH Chemical Genomics Center
Dear Krati,
As it's suggested by the programm, you've an internal coordinate syste= m problem.
So, i advice you to set a new structure of your systemand try to abstr= act an hydrogen atom from a layer when you select the layers=  ( i mean one hydrogen atom will be selected in another layer)
Try that, perhaps it works
Sincerely
Bonoit

--- En date de : Lun 19.9.11, krati joshi kjjuli= e.joshi/./gmail.com <owner-chemistry%%ccl.net> a =E9crit&nb= sp;:

De: krati joshi kjjulie.joshi/./gmail.com <own= er-chemistry%%ccl.net>
Objet: CCL:G: Problem in preparing a proper inp= ut geometry for ONIOM calculations
=C0: "Bonoir, Bonoir " <bon= oit_10%%yahoo.fr>
Date: Lundi 19 septembre 2011, 13h56

Hello sir,
           &nbs= p;  Thanks for the suggestion. I checked the output file but i found t= hat all the values are ok. I am providing you small portion of my outp= ut file 
           &nbs= p;  as follows-
 
 Eigenvalue   256 is   5.23D-07 should be les= s than     0.000000 Eigenvector:
   &= nbsp;           &nbs= p;         D3195   &= nbsp; D1317     D1333     D1325&nbs= p;    D1337
   1     &= nbsp;           &nbs= p;  0.48429   0.36738  -0.30987  -0.29524  -0= .29485
           = ;            &n= bsp; D3203     D1321     D3207 = ;    D3197      R11
   1            &= nbsp;      -0.27254   0.26387  -0.2= 0482  -0.19972  -0.16424
 Eigenvalue   257 is&n= bsp;  4.63D-07 should be less than     0.000000 Ei= genvector:
          &= nbsp;           &nbs= p;  D1325     D3199     D1329&= nbsp;    D3201     D3207
  = 1            &= nbsp;       0.53407   0.39381 = -0.37243  -0.36063  -0.30389
     &n= bsp;            = ;       D1337     D1333      R11      D319= 5     D3203
   1    &n= bsp;            = ;  -0.23305  -0.18893  -0.14606   0.10917  -0= .09532
 Eigenvalue   258 is   4.06D-07 should b= e less than     0.000000 Eigenvector:
  &n= bsp;            = ;          D1333  &n= bsp;  D1329     D1317     D132= 5     D3199
   1    &n= bsp;            = ;   0.60892  -0.34587   0.31007  -0.29786&nbs= p;  0.22521
          &nb= sp;            =   D3203     D1321      R1= 1       R6      = ; D3207
   1        &n= bsp;          -0.21351  -= 0.20886  -0.18784  -0.15529  -0.15423
 Eigenvalue&nb= sp;  259 is   2.81D-07 should be less than   =   0.000000 Eigenvector:
       &= nbsp;           &nbs= p;     D1329     D3197  &= nbsp;  D3203     D3205    &nbs= p; R16
   1            &= nbsp;       0.35545   0.34698 = -0.30807   0.30120  -0.26150
    &nb= sp;            =         D1317     D3= 201      R17      D1325&n= bsp;     R4
   1    &n= bsp;            = ;  -0.21696  -0.21311  -0.21273  -0.19237  -0.1861= 5
 Eigenvalue   260 is   2.31D-07 should be les= s than     0.000000 Eigenvector:
   &= nbsp;           &nbs= p;         D1341     D1321     D1325 &nb= sp;   D3205     D1317
   1 =             &nb= sp;      0.45403   0.42095  -0.3028= 8  -0.28021  -0.27618
      &nbs= p;            &= nbsp;     D1329     D3199 &nbs= p;    R11      D3207  &nb= sp;   R6
   1      &nb= sp;            -0.26= 705   0.24524   0.20178  -0.16533   0.16= 409
 Eigenvalue   261 is   1.79D-07 should be l= ess than     0.000000 Eigenvector:
         &nbs= p;            &= nbsp;   R16       R17  &n= bsp;    R13       R12 &nb= sp;    D3199
   1     =             &nb= sp;  0.43305   0.39082   0.25109  -0.23849&nb= sp;  0.21929
         =             &nb= sp;    R11       R4  = ;     D1337     D1317  &n= bsp;  D3201
   1       = ;            -0.18287   0.17637   0.17231  -0.16282  -0.1= 5542
 Eigenvalue   262 is   1.53D-07 should be = less than     0.000000 Eigenvector:
  &nbs= p;            &= nbsp;          R11  =      R4       D3201 =     D1317      R7
   1=             &nb= sp;       0.72761   0.28931  -= 0.19429   0.16647   0.14439
    =             &nb= sp;        D3203    = D1341     D3207      R13      D3205
   1   = ;            &n= bsp;   -0.14225  -0.13633  -0.13097   0.12776=    0.12450
 Eigenvalue   263 is   1.0= 7D-07 should be less than     0.000000 Eigenvector:
=             &nb= sp;            = R13       R6     &n= bsp;  R17       R8   &nbs= p;    R22
   1     &nb= sp;            =   0.50511  -0.49306  -0.28162   0.19005  -0.16163
          &n= bsp;            = ;   R24       R14   =     R27       R18  &= nbsp;   D1321
   1     &nbs= p;            &= nbsp; 0.15881  -0.15067   0.14746  -0.13866  = 0.13633
 NTrRot=3D  4233 NTRed=3D  4479 NAtoms=3D &= nbsp;  84 NSkip=3D  4233 IsLin=3DF
 Error in internal coo= rdinate system.
 Error termination via Lnk1e in /home/raj/gaussian0= 9//g09/l103.exe at Sun Sep 18 03:24:21 2011.
 Job cpu time:  0= days  8 hours 41 minutes 38.2 seconds.
 File lengths (MBytes)= :  RWF=3D    818 Int=3D      0 D2E=3D      0 Chk=3D    270 Scr=3D=       1
 
 My input file looks like-
 
%mem=3D2500MB
%chk=3DQ025-ONICAL2-70.chk
#p opt oniom(b3lyp/dgdzvp:uff) nosymm geom=3Dconnect
Q025-cal2-70
0 1 0 1 0 1
Si-Si3 0 -0.36206632 0.54077205 -0.51931236 H
O-O_2 0 1.19460468 0.78686805 -0.06577136 H
O-O_2 0 -1.20290432 0.77435105 0.88184164 H
O-O_2 0 -0.44703432 -1.04638495 -0.95862036 H
O-O_2 0 -0.84419432 1.59445505 -1.69660236 H
 
If u have some time pls look into the matter and  give me so= me suggestions pls.Thanks in advance.
 
 
Krati Joshi
NCL Pune