From owner-chemistry@ccl.net Fri May 22 00:33:00 2009 From: "Marek Maly marek.maly{:}ujep.cz" To: CCL Subject: CCL: SOS - problem with Tinker pbsxyz routine Message-Id: <-39353-090522002136-24658-AwYmHlWwywaDr900rWo5Hw]^[server.ccl.net> X-Original-From: "Marek Maly" Content-Transfer-Encoding: 8bit Content-Type: text/plain; format=flowed; delsp=yes; charset=iso-8859-2 Date: Fri, 22 May 2009 06:21:25 +0200 MIME-Version: 1.0 Sent to CCL by: "Marek Maly" [marek.maly^ujep.cz] Dear all, I just started with Tinker (Windows version 4.2 + Force Field Explorer v. 5) and I had problems from the very begining. First of all Tinker commands (minimize, analyze ...) do not appear (I don't know why) in the Force Field Explorer (FFE) "Modeling Commands" menu (there are only 3 commands available - PDBXYZ, Nucleic, Protein commands ). But OK I quickly found out that this is not crucial problem since Tinker routines is possible to run from the command line. So I started some simple tests like minimisation of the 1 molecule of methanol .... But I always got the same errors: "Atoms with an unusual number of attached atoms" followed by error "Some required potential energy parameters are undefined". It was pretty crushing especially when Tinker analysis of all my simple testing molecules using WebMo interface ( http://buchner.chem.hope.edu/~webmodemo/cgi-bin/webmo/jobmgr.cgi ) finished successfully as well as arbitrary of the test or example system which is the part of the Tinker instalation. Later I found where the problem is since between the test cases which are distributed with the Tinker/FFE instalation is also present butane, here is it's XYZ file. ###XYZ file of BUTANE from the TEST directory of the Tinker instalation 14 Butane (Transoid Conformer) 1 C 0.000000 0.000000 0.000000 1 2 5 6 7 2 C 0.000000 0.000000 1.534070 1 1 3 8 9 3 C 1.420290 0.000000 2.119727 1 2 4 10 11 4 C 1.420290 0.000000 3.653797 1 3 12 13 14 5 H -1.036686 0.000000 -0.406075 5 1 6 H 0.515799 -0.897665 -0.409019 5 1 7 H 0.515799 0.897665 -0.409019 5 1 8 H -0.554266 -0.894455 1.901714 5 2 9 H -0.554266 0.894455 1.901714 5 2 10 H 1.974556 0.894455 1.752082 5 3 11 H 1.974556 -0.894455 1.752082 5 3 12 H 2.456977 0.000000 4.059869 5 4 13 H 0.904492 -0.897664 4.062818 5 4 14 H 0.904492 0.897664 4.062818 5 4 So I took my PDB file of the butane (which I created outside of Tinker) ### PDB file of the BUTANE ATOM 1 C MOL 1 -5.559 1.660 -0.150 1.00 0.00 C ATOM 2 C MOL 1 -4.228 2.402 0.075 1.00 0.00 C ATOM 3 C MOL 1 -3.240 1.465 0.794 1.00 0.00 C ATOM 4 C MOL 1 -1.911 2.208 1.024 1.00 0.00 C ATOM 5 H MOL 1 -5.378 0.744 -0.803 1.00 0.00 H ATOM 6 H MOL 1 -6.298 2.356 -0.667 1.00 0.00 H ATOM 7 H MOL 1 -5.984 1.333 0.855 1.00 0.00 H ATOM 8 H MOL 1 -4.411 3.324 0.719 1.00 0.00 H ATOM 9 H MOL 1 -3.793 2.720 -0.930 1.00 0.00 H ATOM 10 H MOL 1 -3.055 0.542 0.151 1.00 0.00 H ATOM 11 H MOL 1 -3.677 1.148 1.798 1.00 0.00 H ATOM 12 H MOL 1 -1.478 2.533 0.020 1.00 0.00 H ATOM 13 H MOL 1 -1.174 1.516 1.550 1.00 0.00 H ATOM 14 H MOL 1 -2.098 3.128 1.671 1.00 0.00 H and converted it using Tinker pdbxyz routine (used mm3 forcefield) so I have obtained this xyz file. ###XYZ file of BUTANE obtained from the above PDB file using pdbxyz routine. 14 1 C -5.559000 1.660000 -0.150000 0 2 5 6 7 2 C -4.228000 2.402000 0.075000 0 1 3 8 9 3 C -3.240000 1.465000 0.794000 0 2 4 10 11 4 C -1.911000 2.208000 1.024000 0 3 12 13 14 5 H -5.378000 0.744000 -0.803000 0 1 6 H -6.298000 2.356000 -0.667000 0 1 7 H -5.984000 1.333000 0.855000 0 1 8 H -4.411000 3.324000 0.719000 0 2 9 H -3.793000 2.720000 -0.930000 0 2 10 H -3.055000 0.542000 0.151000 0 3 11 H -3.677000 1.148000 1.798000 0 3 12 H -1.478000 2.533000 0.020000 0 4 13 H -1.174000 1.516000 1.550000 0 4 14 H -2.098000 3.128000 1.671000 0 4 It is pretty clear that problem is in the 6th column which probably represents atom types ? I checked all my experiments and in all cases, the sixth column are zeros in contrast with provided test cases. I will be really grateful for any suggestion/info which could help me soon to solve this strange/unplesant problem. Thanks very much in advance ! Marek -- Tato zpráva byla vytvořena převratným poątovním klientem Opery: http://www.opera.com/mail/ From owner-chemistry@ccl.net Fri May 22 01:48:00 2009 From: "Kalju Kahn kalju..chem.ucsb.edu" To: CCL Subject: CCL: SOS - problem with Tinker pbsxyz routine Message-Id: <-39354-090522014515-23712-Zth+j6hYDj9Szpw3PNEBUw**server.ccl.net> X-Original-From: "Kalju Kahn" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Thu, 21 May 2009 22:44:59 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: "Kalju Kahn" [kalju(a)chem.ucsb.edu] Hi Marek, I have found MOLDEN more useful than the Force Field Explorer for preparing input for TINKER. MOLDEN does the atom type assignments for you, and does it well, IMHO. However, you have to hope that the necessary MM3 parameters for your organic molecule are defined in the Tinker MM3 force field file (methanol and butane will work, methyl butanoate will not). You can easily launch Tinker minimizations (and with a recent--April 2009-- version also saddle point searches) from within MOLDEN after defining the TNK_ROOT environment. It will work in Windows, but you need to run it via X-terminal emulator ... much easier if you just do it under Linux (LiveCD?). Take a look at some brief tutorials at: http://www.chem.ucsb.edu/~kalju/chem126/public/molecules_zmatrix.html and http://www.chem.ucsb.edu/~kalju/chem126/public/molecules_confanal.html Hope this helps, Kalju > > Sent to CCL by: "Marek Maly" [marek.maly^ujep.cz] > Dear all, > > I just started with Tinker (Windows version 4.2 + Force Field Explorer v. > 5) and I had problems from the very begining. > First of all Tinker commands (minimize, analyze ...) do not appear (I > don't know why) in the Force Field Explorer (FFE) "Modeling Commands" menu > (there are only 3 commands available - PDBXYZ, Nucleic, Protein commands > ). But OK I quickly found out that this > is not crucial problem since Tinker routines is possible to run from the > command line. > > So I started some simple tests like minimisation of the 1 molecule of > methanol .... > > But I always got the same errors: "Atoms with an unusual number of > attached atoms" followed > by error "Some required potential energy parameters are undefined". > > It was pretty crushing especially when Tinker analysis of all my simple > testing molecules using WebMo > interface ( > http://buchner.chem.hope.edu/~webmodemo/cgi-bin/webmo/jobmgr.cgi ) > finished successfully as well > as arbitrary of the test or example system which is the part of the Tinker > instalation. > > > Later I found where the problem is since between the test cases which are > distributed with the Tinker/FFE instalation > is also present butane, here is it's XYZ file. > > ###XYZ file of BUTANE from the TEST directory of the Tinker instalation > 14 Butane (Transoid Conformer) > 1 C 0.000000 0.000000 0.000000 1 2 5 > 6 7 > 2 C 0.000000 0.000000 1.534070 1 1 3 > 8 9 > 3 C 1.420290 0.000000 2.119727 1 2 4 10 > 11 > 4 C 1.420290 0.000000 3.653797 1 3 12 13 > 14 > 5 H -1.036686 0.000000 -0.406075 5 1 > 6 H 0.515799 -0.897665 -0.409019 5 1 > 7 H 0.515799 0.897665 -0.409019 5 1 > 8 H -0.554266 -0.894455 1.901714 5 2 > 9 H -0.554266 0.894455 1.901714 5 2 > 10 H 1.974556 0.894455 1.752082 5 3 > 11 H 1.974556 -0.894455 1.752082 5 3 > 12 H 2.456977 0.000000 4.059869 5 4 > 13 H 0.904492 -0.897664 4.062818 5 4 > 14 H 0.904492 0.897664 4.062818 5 4 > > So I took my PDB file of the butane (which I created outside of Tinker) > > ### PDB file of the BUTANE > ATOM 1 C MOL 1 -5.559 1.660 -0.150 1.00 > 0.00 C > ATOM 2 C MOL 1 -4.228 2.402 0.075 1.00 > 0.00 C > ATOM 3 C MOL 1 -3.240 1.465 0.794 1.00 > 0.00 C > ATOM 4 C MOL 1 -1.911 2.208 1.024 1.00 > 0.00 C > ATOM 5 H MOL 1 -5.378 0.744 -0.803 1.00 > 0.00 H > ATOM 6 H MOL 1 -6.298 2.356 -0.667 1.00 > 0.00 H > ATOM 7 H MOL 1 -5.984 1.333 0.855 1.00 > 0.00 H > ATOM 8 H MOL 1 -4.411 3.324 0.719 1.00 > 0.00 H > ATOM 9 H MOL 1 -3.793 2.720 -0.930 1.00 > 0.00 H > ATOM 10 H MOL 1 -3.055 0.542 0.151 1.00 > 0.00 H > ATOM 11 H MOL 1 -3.677 1.148 1.798 1.00 > 0.00 H > ATOM 12 H MOL 1 -1.478 2.533 0.020 1.00 > 0.00 H > ATOM 13 H MOL 1 -1.174 1.516 1.550 1.00 > 0.00 H > ATOM 14 H MOL 1 -2.098 3.128 1.671 1.00 > 0.00 H > > and converted it using Tinker pdbxyz routine (used mm3 forcefield) so I > have obtained > this xyz file. > > > ###XYZ file of BUTANE obtained from the above PDB file using pdbxyz > routine. > 14 > 1 C -5.559000 1.660000 -0.150000 0 2 5 > 6 7 > 2 C -4.228000 2.402000 0.075000 0 1 3 > 8 9 > 3 C -3.240000 1.465000 0.794000 0 2 4 10 > 11 > 4 C -1.911000 2.208000 1.024000 0 3 12 13 > 14 > 5 H -5.378000 0.744000 -0.803000 0 1 > 6 H -6.298000 2.356000 -0.667000 0 1 > 7 H -5.984000 1.333000 0.855000 0 1 > 8 H -4.411000 3.324000 0.719000 0 2 > 9 H -3.793000 2.720000 -0.930000 0 2 > 10 H -3.055000 0.542000 0.151000 0 3 > 11 H -3.677000 1.148000 1.798000 0 3 > 12 H -1.478000 2.533000 0.020000 0 4 > 13 H -1.174000 1.516000 1.550000 0 4 > 14 H -2.098000 3.128000 1.671000 0 4 > > It is pretty clear that problem is in the 6th column which probably > represents atom types ? > > I checked all my experiments and in all cases, the sixth column are zeros > in contrast with provided > test cases. I will be really grateful for any suggestion/info which could > help me soon to solve this > strange/unplesant problem. > > Thanks very much in advance ! > > Marek > > > > -- > Tato zpráva byla vytvořena převratným poątovním klientem Opery: > http://www.opera.com/mail/> > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry UC Santa Barbara, CA 93106 From owner-chemistry@ccl.net Fri May 22 08:33:01 2009 From: "uttama mukherjee uttamachemistry/./gmail.com" To: CCL Subject: CCL:G: computational chemistry Message-Id: <-39355-090522023125-14915-HZ2xWl9tZlzbiVvJMwM6ig^server.ccl.net> X-Original-From: "uttama mukherjee" Date: Fri, 22 May 2009 02:31:21 -0400 Sent to CCL by: "uttama mukherjee" [uttamachemistry__gmail.com] How to work on the computational studies of high energy ionic liquids using gaussian. uttama mukherjee. uttamachemistry[a]gmail.com From owner-chemistry@ccl.net Fri May 22 10:40:01 2009 From: "tran van tan tvtan|-|staff.dthu.edu.vn" To: CCL Subject: CCL:G: need help in gaussian ts search Message-Id: <-39356-090522092634-32269-CWjJuFNrIM0vTRYF8TofBw^server.ccl.net> X-Original-From: "tran van tan" Date: Fri, 22 May 2009 09:26:30 -0400 Sent to CCL by: "tran van tan" [tvtan[a]staff.dthu.edu.vn] Hello everybody! I want to find a transition state in gaussian with this input # opt=(calcfc,tight,gdiis,ts) freq ub3lyp/6-311+g(d,p) nosymm ts 0 2 C C 1 B1 H 2 B2 1 A1 C 1 B3 2 A2 3 D1 N 4 B4 1 A3 2 D2 H 4 B5 1 A4 2 D3 B1 1.19117810 B2 1.05686011 B3 1.42940095 B4 1.24698289 B5 1.08948293 A1 179.42682237 A2 178.40506719 A3 123.91641107 A4 49.00000000 D1 180.00000000 D2 180.00000000 D3 0.00000000 but the the result is not the transition state i want to find I also use qst2 method in gaussian but the result is not different # opt=qst2 b3lyp/6-311+g(d,p) freq re 0 2 C C 1 B1 H 2 B2 1 A1 C 1 B3 2 A2 3 D1 N 4 B4 1 A3 2 D2 H 4 B5 1 A4 2 D3 B1 1.19117810 B2 1.05686011 B3 1.42940095 B4 1.24698289 B5 1.08948293 A1 179.42682237 A2 178.40506719 A3 123.91641107 A4 117.46164804 D1 180.00000000 D2 180.00000000 D3 0.00000000 Can you help me to find out my true transition state best regard From owner-chemistry@ccl.net Fri May 22 12:11:00 2009 From: "Anthony J. H. M. Meijer a.meijer(_)sheffield.ac.uk" To: CCL Subject: CCL: Questionnaire (UK mainly) Message-Id: <-39357-090522111743-26331-1M5E3iT08RCUhza1A/Rirw|*|server.ccl.net> X-Original-From: "Anthony J. H. M. Meijer" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 22 May 2009 15:39:42 +0100 MIME-Version: 1.0 Sent to CCL by: "Anthony J. H. M. Meijer" [a.meijer:sheffield.ac.uk] (Apologies if people get this twice) Dear Colleagues, Computational Collaborative Project on Quantum Dynamics (CCP6) in the UK is contemplating to run a workshop on the codes that were developed and/or supported within its framework. See http://www.ccp6.ac.uk/downloads.htm Provisionally the workshop is to be held in September 2009 at either Daresbury Lab or Sheffield University. The training will be offered either for free or for a nominal charge. In order to assess whether there is sufficient interest in doing this we would highly appreciate if interested parties could answer the following questions. 1. Which codes are you interested in? [ ] ABC [ ] ABCD [ ] BOUND [ ] DVR3D [ ] MCTDH [ ] MOLSCAT [ ] MULTIMODE [ ] WAVR4 [ ] other (indicate) 2. Timeframe for the workshop [ ] September 2009 [ ] other (indicate) 3. Venue [ ] Daresbury [ ] Sheffield [ ] does not matter [ ] other (indicate) Please respond to Igor Kozin, STFC Daresbury Lab igor.kozin (at) stfc.ac.uk with the subject line "CCP6 workshop" no later than the end of May 2009. Feel free to forward this email. Greetings, Anthony Meijer -- -------------------------------------------------------------------------------- Dr. Anthony J. H. M. Meijer Email: a.meijer^-^sheffield.ac.uk Dept. of Chemistry, Room G8a WWW: meijer.group.shef.ac.uk University of Sheffield Tel:+44-114-222-9482 Sheffield S3 7HF Fax:+44-114-222-9346 United Kingdom PGP:0xB55B90AF -------------------------------------------------------------------------------- A truly wise man never plays leapfrog with a unicorn. From owner-chemistry@ccl.net Fri May 22 13:02:00 2009 From: "Imran Predhanekar imranpkm[#]gmail.com" To: CCL Subject: CCL: Coulomb Hole Message-Id: <-39358-090522125953-880-r0WtUc0cu3KQJ0sCan23UQ%x%server.ccl.net> X-Original-From: "Imran Predhanekar" Date: Fri, 22 May 2009 12:59:49 -0400 Sent to CCL by: "Imran Predhanekar" [imranpkm{}gmail.com] Dear All, Can someone give tips on calculating coulomb hole from optimised geometries. Or is there any tutorial or method on calculating coulomb hole from optimised geometry. Thanks in advance and regards Imran From owner-chemistry@ccl.net Fri May 22 17:00:01 2009 From: "Marek Maly marek.maly^^^ujep.cz" To: CCL Subject: CCL: SOS - problem with Tinker pbsxyz routine Message-Id: <-39359-090522165143-5545-IsJaOMXxN1GVcr0xxUhiwA|-|server.ccl.net> X-Original-From: "Marek Maly" Content-Transfer-Encoding: 8bit Content-Type: text/plain; format=flowed; delsp=yes; charset=utf-8 Date: Fri, 22 May 2009 22:51:34 +0200 MIME-Version: 1.0 Sent to CCL by: "Marek Maly" [marek.maly,+,ujep.cz] Hi Kalju, thanks a lot for your advice. Molden in combination with Tinker seems promissing. As I learned from prof. Ponder, problem is that the Tinker is not capable to assign ff atom types automaticaly to arbitrary molecule. Automatic atom type assignments are available only in case of proteins and nucleic acids. As I already wrote him, this reasoning didn't came on my mind since first of all I am working with Amber, where Antechamber does this work (of course just regarding to Amber ff/Gaff) and secondly as I already mentioned, Tinker (with mm3 ffc) used via WebMo interface ( http://buchner.chem.hope.edu/~webmodemo/cgi-bin/webmo/jobmgr.cgi ) perfectly processed my butane PDB and calculated its energy so they probably use some automatic way to assign atom types ... so I thaught, that pdbxyz routine should do the similar job like Antechamber (regarding to atom type assignments). OK anyway, I am looking for some MM SW which is able to use mainly Amber forcefields/Gaff to help me derive some missing Amber ff parameters in case of "nonstandard" compounds like Si by fitting MM relative energies, rotational profiles using QM ones. It seems to me that Molden+Tinker could be a good candidate for this kind of job, but if you know something better, please just let me know. Thanks again ! Best, Marek Dne Fri, 22 May 2009 07:44:59 +0200 Kalju Kahn kalju..chem.ucsb.edu napsal/-a: > > Sent to CCL by: "Kalju Kahn" [kalju(a)chem.ucsb.edu] > Hi Marek, > > I have found MOLDEN more useful than the Force Field Explorer for > preparing input for TINKER. MOLDEN does the atom type assignments for > you, and does it well, IMHO. However, you have to hope that the > necessary MM3 parameters for your organic molecule are defined in the > Tinker MM3 force field file (methanol and butane will work, methyl > butanoate will not). > > You can easily launch Tinker minimizations (and with a recent--April > 2009-- version also saddle point searches) from within MOLDEN after > defining the TNK_ROOT environment. It will work in Windows, but you need > to run it via X-terminal emulator ... much easier if you just do it under > Linux (LiveCD?). > > Take a look at some brief tutorials at: > > http://www.chem.ucsb.edu/~kalju/chem126/public/molecules_zmatrix.html > > and > > http://www.chem.ucsb.edu/~kalju/chem126/public/molecules_confanal.html > > > Hope this helps, > > Kalju > > >> >> Sent to CCL by: "Marek Maly" [marek.maly^ujep.cz] >> Dear all, >> >> I just started with Tinker (Windows version 4.2 + Force Field Explorer >> v. >> 5) and I had problems from the very begining. >> First of all Tinker commands (minimize, analyze ...) do not appear (I >> don't know why) in the Force Field Explorer (FFE) "Modeling Commands" >> menu >> (there are only 3 commands available - PDBXYZ, Nucleic, Protein commands >> ). But OK I quickly found out that this >> is not crucial problem since Tinker routines is possible to run from the >> command line. >> >> So I started some simple tests like minimisation of the 1 molecule of >> methanol .... >> >> But I always got the same errors: "Atoms with an unusual number of >> attached atoms" followed >> by error "Some required potential energy parameters are undefined". >> >> It was pretty crushing especially when Tinker analysis of all my simple >> testing molecules using WebMo >> interface ( >> http://buchner.chem.hope.edu/~webmodemo/cgi-bin/webmo/jobmgr.cgi ) >> finished successfully as well >> as arbitrary of the test or example system which is the part of the >> Tinker >> instalation. >> >> >> Later I found where the problem is since between the test cases which >> are >> distributed with the Tinker/FFE instalation >> is also present butane, here is it's XYZ file. >> >> ###XYZ file of BUTANE from the TEST directory of the Tinker instalation >> 14 Butane (Transoid Conformer) >> 1 C 0.000000 0.000000 0.000000 1 2 5 >> 6 7 >> 2 C 0.000000 0.000000 1.534070 1 1 3 >> 8 9 >> 3 C 1.420290 0.000000 2.119727 1 2 4 10 >> 11 >> 4 C 1.420290 0.000000 3.653797 1 3 12 13 >> 14 >> 5 H -1.036686 0.000000 -0.406075 5 1 >> 6 H 0.515799 -0.897665 -0.409019 5 1 >> 7 H 0.515799 0.897665 -0.409019 5 1 >> 8 H -0.554266 -0.894455 1.901714 5 2 >> 9 H -0.554266 0.894455 1.901714 5 2 >> 10 H 1.974556 0.894455 1.752082 5 3 >> 11 H 1.974556 -0.894455 1.752082 5 3 >> 12 H 2.456977 0.000000 4.059869 5 4 >> 13 H 0.904492 -0.897664 4.062818 5 4 >> 14 H 0.904492 0.897664 4.062818 5 4 >> >> So I took my PDB file of the butane (which I created outside of Tinker) >> >> ### PDB file of the BUTANE >> ATOM 1 C MOL 1 -5.559 1.660 -0.150 1.00 >> 0.00 C >> ATOM 2 C MOL 1 -4.228 2.402 0.075 1.00 >> 0.00 C >> ATOM 3 C MOL 1 -3.240 1.465 0.794 1.00 >> 0.00 C >> ATOM 4 C MOL 1 -1.911 2.208 1.024 1.00 >> 0.00 C >> ATOM 5 H MOL 1 -5.378 0.744 -0.803 1.00 >> 0.00 H >> ATOM 6 H MOL 1 -6.298 2.356 -0.667 1.00 >> 0.00 H >> ATOM 7 H MOL 1 -5.984 1.333 0.855 1.00 >> 0.00 H >> ATOM 8 H MOL 1 -4.411 3.324 0.719 1.00 >> 0.00 H >> ATOM 9 H MOL 1 -3.793 2.720 -0.930 1.00 >> 0.00 H >> ATOM 10 H MOL 1 -3.055 0.542 0.151 1.00 >> 0.00 H >> ATOM 11 H MOL 1 -3.677 1.148 1.798 1.00 >> 0.00 H >> ATOM 12 H MOL 1 -1.478 2.533 0.020 1.00 >> 0.00 H >> ATOM 13 H MOL 1 -1.174 1.516 1.550 1.00 >> 0.00 H >> ATOM 14 H MOL 1 -2.098 3.128 1.671 1.00 >> 0.00 H >> >> and converted it using Tinker pdbxyz routine (used mm3 forcefield) so I >> have obtained >> this xyz file. >> >> >> ###XYZ file of BUTANE obtained from the above PDB file using pdbxyz >> routine. >> 14 >> 1 C -5.559000 1.660000 -0.150000 0 2 5 >> 6 7 >> 2 C -4.228000 2.402000 0.075000 0 1 3 >> 8 9 >> 3 C -3.240000 1.465000 0.794000 0 2 4 10 >> 11 >> 4 C -1.911000 2.208000 1.024000 0 3 12 13 >> 14 >> 5 H -5.378000 0.744000 -0.803000 0 1 >> 6 H -6.298000 2.356000 -0.667000 0 1 >> 7 H -5.984000 1.333000 0.855000 0 1 >> 8 H -4.411000 3.324000 0.719000 0 2 >> 9 H -3.793000 2.720000 -0.930000 0 2 >> 10 H -3.055000 0.542000 0.151000 0 3 >> 11 H -3.677000 1.148000 1.798000 0 3 >> 12 H -1.478000 2.533000 0.020000 0 4 >> 13 H -1.174000 1.516000 1.550000 0 4 >> 14 H -2.098000 3.128000 1.671000 0 4 >> >> It is pretty clear that problem is in the 6th column which probably >> represents atom types ? >> >> I checked all my experiments and in all cases, the sixth column are >> zeros >> in contrast with provided >> test cases. I will be really grateful for any suggestion/info which >> could >> help me soon to solve this >> strange/unplesant problem. >> >> Thanks very much in advance ! >> >> Marek >> >> >> >> -- >> Tato zpráva byla vytvoøena pøevratnĂ˝m poÂątovnĂ­m klientem Opery: >> http://www.opera.com/mail/> >> >> > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Dr. Kalju Kahn > Department of Chemistry and Biochemistry > UC Santa Barbara, CA 93106> > > > __________ Informace od NOD32 4051 (20090504) __________ > > Tato zprava byla proverena antivirovym systemem NOD32. > http://www.nod32.cz > > -- Tato zpráva byla vytvoĹ™ena pĹ™evratnĂ˝m poštovnĂ­m klientem Opery: http://www.opera.com/mail/