From owner-chemistry@ccl.net Wed May 3 02:24:00 2006 From: "Madhusudhan N.ch. bioinfo.msn:+:gmail.com" To: CCL Subject: CCL: how to convert multiple molecules in sd file format to mol2 format Message-Id: <-31675-060503010832-17645-+DaUbu0hRhIbMC+bKOHl2g===server.ccl.net> X-Original-From: "Madhusudhan N.ch." Content-Type: multipart/alternative; boundary="----=_Part_2676_8805934.1146629640488" Date: Wed, 3 May 2006 09:44:00 +0530 MIME-Version: 1.0 Sent to CCL by: "Madhusudhan N.ch." [bioinfo.msn-x-gmail.com] ------=_Part_2676_8805934.1146629640488 Content-Type: text/plain; charset=UTF-8; format=flowed Content-Transfer-Encoding: base64 Content-Disposition: inline cmVzcGVjdGVkIHNpciwKaSBhbSBzdHVkZW50IHdhbnQgdG8gdXNlIHRoZSB0b3hpY2l0eSBkYXRh c2V0IHdoaWNoIGFyZSBwcmVzZW50IGluCmNoZW1vaW5mb3JtYXRpY3Mub3JnIHNpdGUKCmJ1dCBt b3N0IG9mIG1vbGVjdWxlcyBhcmUgaW4gc21pbGVzIGZvcm1hdCBvciBzZGYgZm9ybWF0IGhvdyBj YW4gaSB1c2UgdGhlc2UKZGF0YXNldHMgZm9yIFFTQVIgT1IgUVNUUi4KCmhvdyB0byBjb252ZXJ0 IHRoZW0gaW50byBzeWJlbCBtb2wyIGZvcm1hdCBvciBtb2wgZm9ybWF0LgoKY2FuIG9wZW4gYmFi ZWwgZG8gdGhpcwp0aGFua3MgaW4gYWR2YW5jZSBmb3Igc3BlbmRpbmcgdSByICB2YWx1YWJsZSB0 aW1lIGluIHJlcGxheWluZyB0aGlzCgpieQptYWRodQo= ------=_Part_2676_8805934.1146629640488 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: base64 Content-Disposition: inline PGRpdj5yZXNwZWN0ZWQgc2lyLDwvZGl2Pgo8ZGl2PmkgYW0gc3R1ZGVudCB3YW50IHRvIHVzZSB0 aGUgdG94aWNpdHkgZGF0YXNldCB3aGljaCBhcmUgcHJlc2VudCBpbiA8YSBocmVmPSJodHRwOi8v Y2hlbW9pbmZvcm1hdGljcy5vcmciPmNoZW1vaW5mb3JtYXRpY3Mub3JnPC9hPiBzaXRlPC9kaXY+ CjxkaXY+Jm5ic3A7PC9kaXY+CjxkaXY+YnV0IG1vc3Qgb2YgbW9sZWN1bGVzIGFyZSBpbiBzbWls ZXMgZm9ybWF0IG9yIHNkZiBmb3JtYXQgaG93IGNhbiBpIHVzZSB0aGVzZSBkYXRhc2V0cyBmb3Ig UVNBUiBPUiBRU1RSLjwvZGl2Pgo8ZGl2PiZuYnNwOzwvZGl2Pgo8ZGl2PmhvdyB0byBjb252ZXJ0 IHRoZW0gaW50byBzeWJlbCBtb2wyIGZvcm1hdCBvciBtb2wgZm9ybWF0LjwvZGl2Pgo8ZGl2PiZu YnNwOzwvZGl2Pgo8ZGl2PmNhbiBvcGVuIGJhYmVsIGRvIHRoaXM8L2Rpdj4KPGRpdj50aGFua3Mg aW4gYWR2YW5jZSBmb3Igc3BlbmRpbmcgdSByICZuYnNwO3ZhbHVhYmxlIHRpbWUgaW4gcmVwbGF5 aW5nIHRoaXM8L2Rpdj4KPGRpdj4mbmJzcDs8L2Rpdj4KPGRpdj5ieTwvZGl2Pgo8ZGl2Pm1hZGh1 PC9kaXY+Cg== ------=_Part_2676_8805934.1146629640488-- From owner-chemistry@ccl.net Wed May 3 03:38:00 2006 From: "Sigismondo Boschi s.boschi|*|cineca.it" To: CCL Subject: CCL:G: Cartesian Coordinate Transformation Message-Id: <-31676-060503033611-26915-Zbt/rYkIoXpbperNZJy7bQ{:}server.ccl.net> X-Original-From: Sigismondo Boschi Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 3 May 2006 09:35:55 +0200 (MEST) MIME-Version: 1.0 Sent to CCL by: Sigismondo Boschi [s.boschi()cineca.it] Xiaobo Zheng xiaoboccl:+:gmail.com wrote: > Sent to CCL by: "Xiaobo Zheng" [xiaoboccl#%#gmail.com] > Dear CCLer, > > I am using Gaussian to optimized geometries with constraints and my input format is in cartesian coordinate. But after optimization, somtimes, Gaussian output does not contain my original cartesian coordinate information. Instead, it reports "standard orientation", which is a transformation of my original coordinate. I am just wondering if there is an easy way or tools to transform Gaussian "starndard orientation" back to my cartesian coordinate. Hi, I was playing with rotations just in these days... I would do it in this way: - get the inertia tensor I of the original molecule - find the corresponding rotation matrix R that rotate it in its standard orientation, by finding the eigenvalues of I. - apply the inverse of R to the last molecules got from gaussian. The two molecules now should come in a "similar" orientation... you can not state that they are in the same, since the two molecules are different. Just their inertia tensor are in the same orientation. Otherwise, if you want to let the two molecules have a particular group aligned, like a phenyl, you need to play differently with rotations/translations. I hope this helps. Regard, Sigismondo -- ------------------------------------------------------------------------------- User Guide: http://www.cineca.it/sap/files/user_guide_cineca.pdf SUPPORT REQUESTS: superc:cineca.it ** PERSONAL ADDRESS: s.boschi:cineca.it ** ------------------------------------------------------------------------------- Sigismondo Boschi, Ph.D. tel: +39 051 6171559 CINECA (High Performance Systems) fax: +39 051 6137273 - 6132198 via Magnanelli, 6/3 http://instm.cineca.it 40033 Casalecchio di Reno (BO)-ITALY http://www.cineca.it From owner-chemistry@ccl.net Wed May 3 04:12:01 2006 From: "Barry Hardy barry.hardy^^^tiscalinet.ch" To: CCL Subject: CCL: Drug Discovery Advanced Training Week, 3-7 July 2006, Oxford Message-Id: <-31677-060503040053-11538-0DlqCL3CwjWzN888pzCA4Q=-=server.ccl.net> X-Original-From: Barry Hardy Content-Type: multipart/alternative; boundary="=====================_9830525==_.ALT" Date: Wed, 03 May 2006 10:00:33 +0200 Mime-Version: 1.0 Sent to CCL by: Barry Hardy [barry.hardy#,#tiscalinet.ch] --=====================_9830525==_.ALT Content-Type: text/plain; charset="iso-8859-1"; format=flowed Content-Transfer-Encoding: quoted-printable Latest Advances in Drug Discovery Design & Planning Methods, a Hands-on 5=20 Day eCheminfo Advanced Training Workshop Week, takes place 3-7 July 2006;=20 Chemistry Research Laboratory, Oxford University, Oxford, UK You can download a copy of the Program from the Cheminfostream Blog: http://barryhardy.blogs.com/cheminfostream/files/eChemProgramOxford06-v7web.= pdf A bursary of value =A31000 will be used to support the attendance of one=20 academic participant, who may be working in any area of chemistry related=20 to drug discovery. To apply for the bursary please send an email with a) a= =20 description of your research; your training needs (ca. 500 words), b) your= =20 CV to echeminfo [at] douglasconnect.com by 12 May. The recipient of the=20 award will be selected based on an evaluation of the potential impact of=20 the training on their research and will be notified by 19 May. We=20 gratefully acknowledge the sponsorship support of Lhasa Ltd. Academic participants are eligible for a 30% academic discount. Places are= =20 limited so please register early to ensure a place. Further information is available at: http://echeminfo.colayer.net/COMTY_training/ We will use the Chemistry Information Technology Center at the Chemistry=20 Research Laboratory at Oxford University for all workshop sessions. The IT= =20 classroom can be viewed in 3D at: http://www.chem.ox.ac.uk/it/hardware.html best regards Barry Hardy eCheminfo Community of Practice Douglas Connect, Switzerland +41 61 851 0170 (office) --=====================_9830525==_.ALT Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Latest Advances in Drug Discovery Design & Planning Methods, a Hands-on 5 Day eCheminfo Advanced Training Workshop Week, takes place 3-7 July 2006; Chemistry Research Laboratory, Oxford University, Oxford, UK

You can download a copy of the Program from the Cheminfostream=20 Blog:
http://barryhardy.blogs.com/cheminfostream/files/eChemPr= ogramOxford06-v7web.pdf

A bursary of value =A31000 will be used to support the attendance of one academic participant, who may be working in any area of chemistry related to drug discovery.  To apply for the bursary please send an email with a) a description of your research; your training needs (ca. 500 words), b) your CV to echeminfo [at] douglasconnect.com by 12 May.  The recipient of the award will be selected based on an evaluation of the potential impact of the training on their research and will be notified by 19 May.  We gratefully acknowledge the sponsorship support of Lhasa Ltd.

Academic participants are eligible for a 30% academic discount.  Places are limited so please register early to ensure a place.

Further information is available at:
http://echeminfo.colayer.net/COMTY_training/

We will use the Chemistry Information Technology Center at the Chemistry Research Laboratory at Oxford University for all workshop sessions.  The IT classroom can be viewed in 3D at: http://www.chem.ox.ac.uk/it/hardware.html


best regards
Barry Hardy
eCheminfo Community of Practice

Douglas Connect, Switzerland
+41 61 851 0170 (office) --=====================_9830525==_.ALT-- From owner-chemistry@ccl.net Wed May 3 05:16:00 2006 From: "mehdi.bounouar_-_ch.tum.de (Mehdi Bounouar)" To: CCL Subject: CCL: Sorting Question Message-Id: <-31678-060503051139-14444-Opfp0RYGtTO3gCZ2VNCYdg!^!server.ccl.net> X-Original-From: mehdi.bounouar[-]ch.tum.de (Mehdi Bounouar) Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Wed, 3 May 2006 11:11:20 +0200 MIME-Version: 1.0 Sent to CCL by: mehdi.bounouar!=!ch.tum.de (Mehdi Bounouar) I think I should clarify my point of view about DOS commands, and my previous replies first of all I always wonder why people are so on the edge, it looks to me that every answer has a good chance to be taken as a personal attack as I see more often with some exchanges, that looks more and more like the average: "Oh YEAH you think you so SMART ! My ego tells you Bla bla ...." Unfortunately I don't master english well enough do be always crystal clear about my point of view, and e-mail's is a very easy way to get completely misunderstood. This list is about exchanging idea's and solutions so if I have an answer or comment, and even if I try to be carefull I don't want to spend 20min's writing the mail. So I always assume that the person is smart enough with a least some sense of humour. I know this is sometime a mistake, but CCL is also supposed not to be the an average mail list, even if it starts to look like. Now back to this DOS command, what I meant is that very few people uses that thing so if you have a problem, who is going to give you an answer ? to tell the person to RTFM is not a smart move especially if you know or had experience with the way things are documented at the Redmond company. > But if it's *there* and he already has it, why shouldn't he use it? Who am I to decide that ? in case this was a real question ;-) ... If you want to spent time writing all your libraries in fortran or assembler who cares ? (but if it is under GPL or ~equiv. bless you) For my part you can even print the whole thing on paper and use a pair of cissors to do the sort if you think that is convenient. At some point one should only realize that if you are going in a direction using certain tools that were not either specifically designed or general enough you will hit a wall very hard to climb and with not many people out there to help you and a good chance of making mistakes that nobody made before. I personally learned a lot from the diverse answers using different tools, it also helps you to think differently about the approach to the problem and that is what this list is about in my opinion. Mehdi From owner-chemistry@ccl.net Wed May 3 05:57:01 2006 From: "Barry Hardy barry.hardy###tiscalinet.ch" To: CCL Subject: CCL: (Reformatted) Drug Discovery Advanced Training Week, 3-7 July 2006, Oxford Message-Id: <-31679-060503055419-10293-5yEiJFSpWRD6xA5X8eka8w- -server.ccl.net> X-Original-From: Barry Hardy Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1"; format=flowed Date: Wed, 03 May 2006 11:49:58 +0200 Mime-Version: 1.0 Sent to CCL by: Barry Hardy [barry.hardy]*[tiscalinet.ch] (Original message was jumbled so will try to fix with this resend. Jan - not sure what happened with the orig msg.) Latest Advances in Drug Discovery Design & Planning Methods, a Hands-on 5 Day eCheminfo Advanced Training Workshop Week, takes place 3-7 July 2006; Chemistry Research Laboratory, Oxford University, Oxford, UK You can download a copy of the Program from the Cheminfostream Blog: http://barryhardy.blogs.com/cheminfostream/files/eChemProgramOxford06-v7web.pdf A bursary of value £1000 will be used to support the attendance of one academic participant, who may be working in any area of chemistry related to drug discovery. To apply for the bursary please send an email with a) a description of your research; your training needs (ca. 500 words), b) your CV to echeminfo [at] douglasconnect.com by 12 May. The recipient of the award will be selected based on an evaluation of the potential impact of the training on their research and will be notified by 19 May. We gratefully acknowledge the sponsorship support of Lhasa Ltd. Academic participants are eligible for a 30% academic discount. Places are limited so please register early to ensure a place. Further information is available at: http://echeminfo.colayer.net/COMTY_training/ We will use the Chemistry Information Technology Center at the Chemistry Research Laboratory at Oxford University for all workshop sessions. The IT classroom can be viewed in 3D at: http://www.chem.ox.ac.uk/it/hardware.html best regards Barry Hardy eCheminfo Community of Practice Douglas Connect, Switzerland +41 61 851 0170 (office) From owner-chemistry@ccl.net Wed May 3 09:14:01 2006 From: "Robert Duke rduke,,email.unc.edu" To: CCL Subject: CCL: Sorting Question Message-Id: <-31680-060503083835-22742-UD/wejThY3NTOteM5U6AAA : server.ccl.net> X-Original-From: "Robert Duke" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="Windows-1252"; reply-type=original Date: Wed, 3 May 2006 08:38:16 -0400 MIME-Version: 1.0 Sent to CCL by: "Robert Duke" [rduke]*[email.unc.edu] Well, actually the example given WILL work if all your numbers to be sorted are aligned in columns (with decimals, if any, aligned) with blank (x20) spacing, the reason being that the characters sorted either start at the first or a specified column, and blank (x20) collates lower than all the numbers (0x30-0x39, or 0-9). This all assumes ascii, which I presume is reasonably safe these days. HOWEVER, there are indeed shortcomings, and these include an inability to handle scientific notation and incorrect sorting for all negative or mixed negative and positive numbers. This last one would I think be the killer for processing the typical output. I would tend to agree with those who have suggested that if you don't have access to some variety of unix, putting cygwin on the dos box is a reasonable alternative to get a better set of unix-like functionality. If you don't want to write code, a tremendous amount can be done with all those standard unix filters. Regards - Bob Duke ----- Original Message ----- > From: "Peter Pinski peter.pinski-forum- -web.de" To: "Duke, Robert E " Sent: Tuesday, May 02, 2006 9:57 PM Subject: CCL: Sorting Question > Sent to CCL by: Peter Pinski [peter.pinski-forum],[web.de] > Hi, > > I don't know, whether there are different sort versions in different > windows versions, but e.g. on windows xp the sort command, as I already > have pointed out once, SHOULD NOT work because it sorts alphanumerically > and not numerically. In plain speach, 1000 is for the ms dos sort > smaller than 900! > > Of course it's not neccessary to program perl or python or whatever for > doing this task. As also already has been mentioned, an alternative is > the unix sort command, which is able to sort numerically if invoked with > the -g flag. It's possible to specify a field with the -k flag. > > The unix sort for windows may either be used by installing cygwin or > installing the gnu textutils for windows available at > > http://gnuwin32.sourceforge.net/packages/textutils.htm > > I may be started in a dos box. For a list of flags see sort --help. > Maybe it's necessary to rename the file sort.exe in order to avoid a > conflict with the windows sort. > > Again, maybe there are different versions of ms dos sort, but those I > have seen yet will provide wrong results because they sort > alphanumerically rather than numerically. > > Greetings, > Peter Pinski > > > John McKelvey jmmckel-,-attglobal.net schrieb: >> Sent to CCL by: John McKelvey [jmmckel|-|attglobal.net] >> >>> Well I wonder how many people are still (seriously!!) using command line >>> under under Windows for such purposes (not administration). >>> >>> >>> >> With no intention of throwing rocks, I recall getting chastised in grad >> school for not trying the easy solution first... >> >> Cheers.. >> John McKelvey> > > > From owner-chemistry@ccl.net Wed May 3 10:37:00 2006 From: "Karl Irikura karl.irikura*o*nist.gov" To: CCL Subject: CCL:G: Cartesian Coordinate Transformation Message-Id: <-31681-060503090016-26264-uQQQypgINDId3jiHpJLVUw]~[server.ccl.net> X-Original-From: Karl Irikura Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Wed, 03 May 2006 08:18:13 -0400 Mime-Version: 1.0 Sent to CCL by: Karl Irikura [karl.irikura**nist.gov] Hi. I think if you include the "NoSymm" keyword you will avoid the re-orientation (in addition to turning off the use of symmetry). Good luck, Karl At 07:31 PM 5/2/2006, you wrote: >Sent to CCL by: "Xiaobo Zheng" [xiaoboccl#%#gmail.com] >Dear CCLer, > >I am using Gaussian to optimized geometries with constraints and my >input format is in cartesian coordinate. But after optimization, >somtimes, Gaussian output does not contain my original cartesian >coordinate information. Instead, it reports "standard orientation", >which is a transformation of my original coordinate. I am just >wondering if there is an easy way or tools to transform Gaussian >"starndard orientation" back to my cartesian coordinate. > >Thanks for your input. > >Xiaobo Zheng---------------------------------------------- Dr. Karl K. Irikura National Institute of Standards and Technology 100 Bureau Drive, Stop 8380 Gaithersburg, MD 20899-8380 voice: 301-975-2510 fax: 301-869-4020 e-mail: karl.irikura**nist.gov http://www.nist.gov/compchem/ ---------------------------------------------- From owner-chemistry@ccl.net Wed May 3 12:54:00 2006 From: "Sten Nilsson Lill stenil(a)chem.gu.se" To: CCL Subject: CCL:G: Cartesian Coordinate Transformation Message-Id: <-31682-060503121520-32141-Mg8pfjGiQCzjNpv+Rkdt/g^_^server.ccl.net> X-Original-From: "Sten Nilsson Lill" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Wed, 3 May 2006 17:14:25 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: "Sten Nilsson Lill" [stenil__chem.gu.se] Hi, the program ChemCraft (the link to the free lite version is http://www.chemcraftprog.com/lite.html) gives you both the standard orientation and input orientation of your molecule along your optimisation. It has a menu button to show the coordinates, so it's easy to just cut and paste them to your next application. Hope this helps, Sten > Sent to CCL by: Sigismondo Boschi [s.boschi()cineca.it] > Xiaobo Zheng xiaoboccl:+:gmail.com wrote: >> Sent to CCL by: "Xiaobo Zheng" [xiaoboccl#%#gmail.com] >> Dear CCLer, >> >> I am using Gaussian to optimized geometries with constraints and my >> input format is in cartesian coordinate. But after optimization, >> somtimes, Gaussian output does not contain my original cartesian >> coordinate information. Instead, it reports "standard orientation", >> which is a transformation of my original coordinate. I am just >> wondering if there is an easy way or tools to transform Gaussian >> "starndard orientation" back to my cartesian coordinate. > Hi, > > I was playing with rotations just in these days... I would do it in this > way: > > - get the inertia tensor I of the original molecule > - find the corresponding rotation matrix R that rotate it in its > standard orientation, by finding the eigenvalues of I. > - apply the inverse of R to the last molecules got from gaussian. > > The two molecules now should come in a "similar" orientation... you can > not state that they are in the same, since the two molecules are > different. Just their inertia tensor are in the same orientation. > > Otherwise, if you want to let the two molecules have a particular group > aligned, like a phenyl, you need to play differently with > rotations/translations. > > I hope this helps. > > Regard, > Sigismondo > > -- > ------------------------------------------------------------------------------- > User Guide: http://www.cineca.it/sap/files/user_guide_cineca.pdf > SUPPORT REQUESTS: superc+*+cineca.it ** > PERSONAL ADDRESS: s.boschi+*+cineca.it ** > ------------------------------------------------------------------------------- > Sigismondo Boschi, Ph.D. tel: +39 051 6171559 > CINECA (High Performance Systems) fax: +39 051 6137273 - 6132198 > via Magnanelli, 6/3 http://instm.cineca.it > 40033 Casalecchio di Reno (BO)-ITALY http://www.cineca.it> > > > Ph. D. Sten Nilsson Lill Dep. of Chemistry Göteborg University Kemigården 4 S-412 96 Göteborg, Sweden Phone: +46-31-772 2901 Fax: +46-31-772 3840 E-mail: stenil[A]chem.gu.se Alternative e-mail: slill1[A]lsu.edu From owner-chemistry@ccl.net Wed May 3 17:13:01 2006 From: "Jeffrey L Nauss jnauss[a]accelrys.com" To: CCL Subject: CCL: Accelrys Customer Training Workshops for June 2006 Message-Id: <-31683-060503170430-7518-Z3YsMKx9al9LrbT6vUfupQ[-]server.ccl.net> X-Original-From: "Jeffrey L Nauss" Date: Wed, 3 May 2006 17:04:24 -0400 Sent to CCL by: "Jeffrey L Nauss" [jnauss]![accelrys.com] Accelrys Inc. are holding the following training workshops during June. These events are designed to help you get more value from your Accelrys software, helping you to better accomplish your research goals. Costs for the scheduled workshops are 500 per day for all customers. For the on-line presentations, the price is 175 per three hour session for all customers. BURLINGTON, MA Structure-Based Design in Discovery Studio 6 June Protein Modeling in Discovery Studio 7 June Simulation in Discovery Studio 8 June Introduction to Life Science Modeling with Insight II 20 - 21 June Homology-Based Protein Design 22 - 23 June CHARMm 26 - 27 June Structure Based Drug Design with InsightII 28 - 29 June CAMBRIDGE, UK Library Design and Analysis with Cerius2 6 - 7 June QSAR with Cerius2 8 - 9 June Structure Based Drug Design with Cerius2 12 - 13 June Pharmacophore Generation with Catalyst 14 - 15 June PARIS, FRANCE Introduction to Quantum Mechanics Modeling 20 - 21 June Introduction to Polymer Modeling 22 - 23 June ON-LINE WORKSHOPS Introduction to MS Modeling 14 Jun (4pm GMT) Accelrys Gene 19 Jun (3pm PST) Accelrys Gene 20 Jun (7am PST) MacVector 21 Jun (3pm PST) MacVector 22 Jun (7am PST) Introduction to General Modeling using Cerius2 27 Jun (5pm GMT) Further details can be found on our website at http://www.accelrys.com/services/training/general/calendar.html and http://www.accelrys.com/services/training/general/calendar_online.html. Questions regarding scheduling and content should be directed to workshops%accelrys.com -- Jeffrey L. Nauss, Ph.D. Lead Training Scientist Accelrys 10188 Telesis Court, Suite 100 San Diego, CA 92121-4779 Phone: +1-858-799-5555 Fax: +1-858-799-5100 http://www.accelrys.com/training From owner-chemistry@ccl.net Wed May 3 21:49:00 2006 From: "Sengen Sun sengensun#yahoo.com" To: CCL Subject: CCL:G: increasing NStep for partial optimization Message-Id: <-31684-060503132857-29806-a1pVawvH7YU+CIl96GLa3A###server.ccl.net> X-Original-From: Sengen Sun Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Wed, 3 May 2006 09:28:52 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Sengen Sun [sengensun..yahoo.com] In my experinece, there are often converge problems when one or two constraints are applied between two molecules. Your case appears to me to be such a case, as 100 steps are quite a big number if your system is not very big. A possible indication for this converge problem is oscillating energies in your output files. That is, the energy jumps back and forth without a general trend. I was suggested to do something to deal with this problem. But it is too complicated to me as I had too many systems to be examined. As I spent more and more time in this, I found that this problem depends on different software programs, and sometimes on the levels of computation and basis sets. Some products are simply bad doing this kind of things. A good product for this purpose is Spartan. I am quite amazed at its speed and stability, and never have had this annoying converge problem again since I bought it. The only relationship I have with Wavefunctions, Inc. is my purchase of their product - Spartan. I don't have any other relationships with them, neither am I an advertising agent for them. I just want to clarify that. Sengen ----------------------------- Christopher.DeDobbelaere[#]student.ua.ac.be wrote: Dear ccl members, I'm doing some popt jobs in g03 where the constraint during the optimization is the distance between two molecules. The optimization takes some time and stops after 100 steps. I already increased maxcycles but that just increases the cycles per scf step. Is there a way to increase NStep to a larger value? This is the error i get: Optimization stopped. -- Number of steps exceeded, NStep= 100 -- Flag reset to prevent archiving. This are the options i'm using right now: p b1b95/6-311+G* popt(MaxCyc=250) freq iop(1/8=10) Thanks in advance! Greetings, Christopher Undergrad. Student University of Antwerp __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com