From owner-chemistry@ccl.net Mon May 1 03:04:00 2006 From: "neeraj misra misraneeraj++gmail.com" To: CCL Subject: CCL: Converting coordinates Message-Id: <-31635-060430223803-2798-9Ku9DrtZGa/wq7zha+Pfhw-.-server.ccl.net> X-Original-From: "neeraj misra" Content-Type: multipart/alternative; boundary="----=_Part_13309_23377682.1146447691018" Date: Mon, 1 May 2006 07:11:31 +0530 MIME-Version: 1.0 Sent to CCL by: "neeraj misra" [misraneeraj++gmail.com] ------=_Part_13309_23377682.1146447691018 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Better check out this site for conversion: http://dasher.wustl.edu/tinker/ On 5/1/06, Juan Gil dagur99[-]hotmail.com wrote: > > Sent to CCL by: "Juan Gil" [dagur99**hotmail.com] > I'm interested in conversion methods from internal to cartesian > coordinates for academic use. Any information is welcome, thanks a lot. > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > > -- Neeraj Misra PhD Assoc.Prof in Physics Lucknow University 226007 Phone 0522-2740410 (O) 0522-3253647 (R) Cell # 9335333805 ------=_Part_13309_23377682.1146447691018 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline

Better check out this site for conversion:

On 5/1/06, J= uan Gil dagur99[-]hotmail.com <owner-chemistry---ccl.net> wrote:

Sent to CCL by: "Juan = Gil" [dagur99**hotmail.com]I'm interested in conversion methods from internal to cartesian coordinat= es for academic use. Any information is welcome, thanks a lot.

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--
Neeraj = Misra PhD
Assoc.Prof in Physics
Lucknow University 226007
Phone 05= 22-2740410 (O)
&nb= sp; 0522-3253647 (R)
Cell # 9335333805=20 ------=_Part_13309_23377682.1146447691018-- From owner-chemistry@ccl.net Mon May 1 07:32:00 2006 From: "Egon Willighagen e.willighagen{}science.ru.nl" To: CCL Subject: CCL: Converting coordinates Message-Id: <-31636-060501072549-10412-U8CY93a0Mx+piH98FEQ4aA%server.ccl.net> X-Original-From: Egon Willighagen Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="utf-8" Date: Mon, 1 May 2006 09:53:59 +0200 MIME-Version: 1.0 Sent to CCL by: Egon Willighagen [e.willighagen|,|science.ru.nl] On Monday 01 May 2006 01:35, Juan Gil dagur99[-]hotmail.com wrote: > Sent to CCL by: "Juan Gil" [dagur99**hotmail.com] > I'm interested in conversion methods from internal to cartesian coordinates > for academic use. Any information is welcome, thanks a lot. The Chemistry Development Kit [1] provides an open source implementation [2,3] in Java, which might serve as template for other programming languages. Egon 1.http://cdk.sf.net/ 2.http://cdk.sourceforge.net/api/org/openscience/cdk/geometry/CrystalGeometryTools.html 3.http://svn.sourceforge.net/viewcvs.cgi/cdk/trunk/cdk/src/org/openscience/cdk/geometry/ -- e.willighagen|science.ru.nl Cologne University Bioinformatics Center (CUBIC) Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 From owner-chemistry@ccl.net Mon May 1 08:06:02 2006 From: "Richard L. Wood rwoodphd:msn.com" To: CCL Subject: CCL: help needed Message-Id: <-31637-060501074429-17016-s3aSFgcUJsmgpR/ci2TDgA[-]server.ccl.net> X-Original-From: "Richard L. Wood" Date: Mon, 1 May 2006 07:44:27 -0400 Sent to CCL by: "Richard L. Wood" [rwoodphd##msn.com] Hi all, This question isn't a direct computational chemistry question, but an indirect one. So please bear with me. I'm trying to analyze the output of a 1 nanosecond MD calculation that I ran using the program NAMD. Since it's a text file, I could use MS Excel to open it and sort the energies from lowest to highest value, which is what I would like to do. However, MS Excel has a limit of about 65000 lines of text (or rows) that a file can contain. Mine has 2000000 lines of text, so that my file is too big. My workaround is to open the file in MS Word, and cut it into pieces that can be opened in MS Excel. Then I can find the minimum energy fro each piece, save that value, and then when done, find the overall minimum. Once I've done this, I can find the corresponding frame number in the file that contained it, go to the trajectory and save those coordinates. However, as you can imagine, this isn't a very efficient process. My simulation takes about 2 and half hours or so to run, while this analysis takes about two hours to do. I can therefore do about one of these in a day, as I have another non-computational "job" that I am doing. At some point, I will be running some smalled calculations, which will take much less than two hours to run, and so the analysis will take longer than the simulation! My question is this: does anyone know of a spreadsheat program where I can a) import a text file of more than 65000 rows easily, b) can sort a given column of that file, and c) works under Windows and is free? I've tried Quattro Pro, and all the file comes out in a single row! TIA, Richard From owner-chemistry@ccl.net Mon May 1 09:11:00 2006 From: "Serena Povia sp422]|[hermes.cam.ac.uk" To: CCL Subject: CCL: help needed Message-Id: <-31638-060501090626-28589-Usu0dEtqcuEEaU8x86m3Dw[]server.ccl.net> X-Original-From: Serena Povia Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Mon, 1 May 2006 14:06:10 +0100 (BST) MIME-Version: 1.0 Sent to CCL by: Serena Povia [sp422(_)hermes.cam.ac.uk] Dear Rich, I'm sorry to tell you that your problem could be *easily* solved in unix, writing a bash/perl script to grep the energy line you're interested in some way, and sort them, and go back to pick up the energies. It's really a matter of 50 lines of code at most and once it's done everything will be authomatic for the following calculations. if you run your calculations on a unix machine you could even run the analysis script on it an then get your nice data back in windows. I'm learning bash myself and I'll be happy to help. best, serena On Mon, 1 May 2006, Richard L. Wood rwoodphd:msn.com wrote: > Sent to CCL by: "Richard L. Wood" [rwoodphd##msn.com] > Hi all, > > This question isn't a direct computational chemistry question, but an indirect one. So please bear with me. > > I'm trying to analyze the output of a 1 nanosecond MD calculation that I ran using the program NAMD. Since it's a text file, I could use MS Excel to open it and sort the energies from lowest to highest value, which is what I would like to do. However, MS Excel has a limit of about 65000 lines of text (or rows) that a file can contain. Mine has 2000000 lines of text, so that my file is too big. My workaround is to open the file in MS Word, and cut it into pieces that can be opened in MS Excel. Then I can find the minimum energy fro each piece, save that value, and then when done, find the overall minimum. Once I've done this, I can find the corresponding frame number in the file that contained it, go to the trajectory and save those coordinates. > > However, as you can imagine, this isn't a very efficient process. My simulation takes about 2 and half hours or so to run, while this analysis takes about two hours to do. I can therefore do about one of these in a day, as I have another non-computational "job" that I am doing. At some point, I will be running some smalled calculations, which will take much less than two hours to run, and so the analysis will take longer than the simulation! > > My question is this: does anyone know of a spreadsheat program where I can a) import a text file of more than 65000 rows easily, b) can sort a given column of that file, and c) works under Windows and is free? I've tried Quattro Pro, and all the file comes out in a single row! > > TIA, > Richard> > > > From owner-chemistry@ccl.net Mon May 1 10:26:00 2006 From: "Jozsef Csontos jozsefcsontos_-_creighton.edu" To: CCL Subject: CCL: help needed Message-Id: <-31639-060501100903-23307-0AQh6FE/YKWOvV8XugobHA^^^server.ccl.net> X-Original-From: Jozsef Csontos Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Mon, 01 May 2006 09:08:53 -0500 Mime-Version: 1.0 Sent to CCL by: Jozsef Csontos [jozsefcsontos{}creighton.edu] Hi, I can imagine that gnumeric doesn't have this "excel" limitation, but I'm not sure, so why don't you check it. It has ported to windows, too. Good luck, Jozsef On Mon, 2006-05-01 at 08:34 -0400, Richard L. Wood rwoodphd:msn.com wrote: > Sent to CCL by: "Richard L. Wood" [rwoodphd##msn.com] > Hi all, > > This question isn't a direct computational chemistry question, but an indirect one. So please bear with me. > > I'm trying to analyze the output of a 1 nanosecond MD calculation that I ran using the program NAMD. Since it's a text file, I could use MS Excel to open it and sort the energies from lowest to highest value, which is what I would like to do. However, MS Excel has a limit of about 65000 lines of text (or rows) that a file can contain. Mine has 2000000 lines of text, so that my file is too big. My workaround is to open the file in MS Word, and cut it into pieces that can be opened in MS Excel. Then I can find the minimum energy fro each piece, save that value, and then when done, find the overall minimum. Once I've done this, I can find the corresponding frame number in the file that contained it, go to the trajectory and save those coordinates. > > However, as you can imagine, this isn't a very efficient process. My simulation takes about 2 and half hours or so to run, while this analysis takes about two hours to do. I can therefore do about one of these in a day, as I have another non-computational "job" that I am doing. At some point, I will be running some smalled calculations, which will take much less than two hours to run, and so the analysis will take longer than the simulation! > > My question is this: does anyone know of a spreadsheat program where I can a) import a text file of more than 65000 rows easily, b) can sort a given column of that file, and c) works under Windows and is free? I've tried Quattro Pro, and all the file comes out in a single row! > > TIA, > Richard> > > -- Jozsef Csontos, Ph.D. Department of Biomedical Sciences Creighton University, Omaha, NE From owner-chemistry@ccl.net Mon May 1 11:01:01 2006 From: "donna : dbkonline.com" To: CCL Subject: CCL: help needed Message-Id: <-31640-060501093103-10873-43/87Ytm/1lB86ESgOEupQ-,-server.ccl.net> X-Original-From: donna~!~dbkonline.com Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format="flowed" Date: Mon, 01 May 2006 07:53:38 -0500 MIME-Version: 1.0 Sent to CCL by: donna[]dbkonline.com Quoting "Richard L. Wood rwoodphd:msn.com" : What about a perl script or something ? When we did MD simulations of huge trajectories that's what we did... you can either do it on the fly - if you just want to get the lowest ... or create a database a sort it. Donna DBK Development, LLC > Sent to CCL by: "Richard L. Wood" [rwoodphd##msn.com] > Hi all, > > This question isn't a direct computational chemistry question, but an > indirect one. So please bear with me. > > I'm trying to analyze the output of a 1 nanosecond MD calculation > that I ran using the program NAMD. Since it's a text file, I could > use MS Excel to open it and sort the energies from lowest to highest > value, which is what I would like to do. However, MS Excel has a > limit of about 65000 lines of text (or rows) that a file can contain. > Mine has 2000000 lines of text, so that my file is too big. My > workaround is to open the file in MS Word, and cut it into pieces > that can be opened in MS Excel. Then I can find the minimum energy > fro each piece, save that value, and then when done, find the overall > minimum. Once I've done this, I can find the corresponding frame > number in the file that contained it, go to the trajectory and save > those coordinates. > > However, as you can imagine, this isn't a very efficient process. My > simulation takes about 2 and half hours or so to run, while this > analysis takes about two hours to do. I can therefore do about one > of these in a day, as I have another non-computational "job" that I > am doing. At some point, I will be running some smalled > calculations, which will take much less than two hours to run, and so > the analysis will take longer than the simulation! > > My question is this: does anyone know of a spreadsheat program where > I can a) import a text file of more than 65000 rows easily, b) can > sort a given column of that file, and c) works under Windows and is > free? I've tried Quattro Pro, and all the file comes out in a single > row! > > TIA, > Richard> > > > From owner-chemistry@ccl.net Mon May 1 11:36:00 2006 From: "Mark Mackey mark^-^cresset-bmd.com" To: CCL Subject: CCL: FieldTemplater - how to find bound conformations Message-Id: <-31641-060501093507-12492-+D1IAzVPPgWw3z0cvnJZMg(~)server.ccl.net> X-Original-From: "Mark Mackey" Date: Mon, 1 May 2006 09:35:03 -0400 Sent to CCL by: "Mark Mackey" [mark(a)cresset-bmd.com] Cresset BioMolecular Discovery Ltd announces that its FieldTemplater software is now available to download from its web-site for a free one month evaluation. FieldTemplater is a highly advanced pharmacophore and bound conformation hypothesis generator: given three or more active molecules FieldTemplater can with high probability deduce not only the bound conformation of those molecules but also the relative alignment. No protein information is required, so FieldTemplater is especially useful for situations when such data is not available (e.g. for GPCR and ion channel ligands). FieldTemplater works by comparing the molecular electrostatic and steric fields of a set of conformationally explored molecules and identifies conformations of molecules that have the same field pattern. Since the field pattern is a distillate of the important binding information, these overlays represent potential binding conformation hypotheses. The results can be used to compare SAR across series and guide lead optimization. Full documentation with case studies is provided. FieldTemplater requires a set of conformationally explored molecules as input and outputs an ordered list of binding overlay hypotheses. XedeX, our conformational explorer is also available to download free from our web site, so you can generate a diverse set of conformers suitable for input to FieldTemplater. For more information on Cresset's Field descriptors, see: Molecular Field Extrema as Descriptors of Biological Activity: Definition and Validation Tim Cheeseright, Mark Mackey, Sally Rose, and Andy Vinter J. Chem. Inf. Model.; vol 46(2), pp665-676, 2006 Both FieldTemplater and XedeX run on the linux operating system. The software will be made available to qualifying academics at a discounted rate. Further details can be found on our web site http://www.cresset-bmd.com/, and the FieldTemplater evaluation can be found at http://www.cresset-bmd.com/fieldtemplater_demo.html . -- Dr Mark Mackey Cresset BioMolecular Discovery From owner-chemistry@ccl.net Mon May 1 12:11:00 2006 From: "Phil Hultin hultin!^!cc.umanitoba.ca" To: CCL Subject: CCL: help needed (sorting a text file) Message-Id: <-31642-060501103905-6144-DQzx0McggNhffU1SgV3iQA-*-server.ccl.net> X-Original-From: "Phil Hultin" Content-Type: multipart/alternative; boundary="----=_NextPart_000_000C_01C66CFA.EC2158B0" Date: Mon, 1 May 2006 08:40:32 -0500 MIME-Version: 1.0 Sent to CCL by: "Phil Hultin" [hultin a cc.umanitoba.ca] This is a multi-part message in MIME format. ------=_NextPart_000_000C_01C66CFA.EC2158B0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Richard: You don't need to use a spreadsheet to do what you want. Open a windows command prompt and type "help sort" to learn about the old-fashioned DOS command line SORT function. Dr. Philip G. Hultin Associate Professor of Chemistry, University of Manitoba Winnipeg, MB R3T 2N2 hultin[-]cc.umanitoba.ca http://umanitoba.ca/chemistry/people/hultin ------=_NextPart_000_000C_01C66CFA.EC2158B0 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Richard:

You don’t need to use a spreadsheet to do what = you want. Open a windows command prompt and type “help = sort” to learn about the old-fashioned DOS command line SORT = function.

Dr. Philip G. Hultin

Associate Professor of = Chemistry,

University of Manitoba

Winnipeg, MB

R3T 2N2

hultin[-]cc.umanitoba.ca

http://umanitoba.ca/= chemistry/people/hultin

------=_NextPart_000_000C_01C66CFA.EC2158B0-- From owner-chemistry@ccl.net Mon May 1 12:46:08 2006 From: "Jim Kress ccl_nospam/./kressworks.com" To: CCL Subject: CCL: Converting coordinates Message-Id: <-31643-060501121530-2096-5EvX2NUUqLaAoDv/Z6NmZw||server.ccl.net> X-Original-From: "Jim Kress" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 1 May 2006 12:15:05 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam*|*kressworks.com] Routine intxyz.f in Tinker will do what you desire. Jim > -----Original Message----- > From: neeraj misra misraneeraj++gmail.com > [mailto:owner-chemistry!=!ccl.net] > Sent: Monday, May 01, 2006 3:43 AM > To: Kress, Jim > Subject: CCL: Converting coordinates > > Sent to CCL by: "neeraj misra" [misraneeraj++gmail.com] > ------=_Part_13309_23377682.1146447691018 > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > Content-Transfer-Encoding: quoted-printable > Content-Disposition: inline > > Better check out this site for conversion: > > http://dasher.wustl.edu/tinker/ > > > On 5/1/06, Juan Gil dagur99[-]hotmail.com > wrote: > > > > Sent to CCL by: "Juan Gil" [dagur99**hotmail.com] I'm > interested in > > conversion methods from internal to cartesian coordinates > for academic > > use. Any information is welcome, thanks a lot. > > > > > > > > -=3D This is automatically added to each message by the > mailing script > > = > =3D-> > > > > > > > > > -- > Neeraj Misra PhD > Assoc.Prof in Physics > Lucknow University 226007 > Phone 0522-2740410 (O) > 0522-3253647 (R) > Cell # 9335333805 > > ------=_Part_13309_23377682.1146447691018 > Content-Type: text/html; charset=ISO-8859-1 > Content-Transfer-Encoding: quoted-printable > Content-Disposition: inline > >

Better check out this site for conversion:

href=3D"http://dasher.wustl.edu/tinker/">http://dasher.wustl.edu/ti= > nker/

On 5/1/06, class=3D"gmail_sendername">J= uan Gil > dagur99[-]hotmail.com < .net">owner-chemistry.:.ccl.net> wrote: >

MARGIN: 0px 0= px 0px 0.8ex; BORDER-LEFT: #ccc 1px > solid">Sent to CCL by: "Juan = Gil" > [dagur99**hotmail.com] r>I'm interested in conversion methods from internal to cartesian > r>coordinat= > es for academic use. Any information is welcome, thanks a lot. >

-=3D This is automatically added to each > message by the mai= ling script =3D-
To recover the email > address of the author of the messa= ge, please change
the > strange characters on the top line to the .:. sign. = You can > also
E-mail to = > subscribers: href=3D"mailto:CHEMISTRY.:.ccl.net">CHEMISTRY.:.ccl.net > or = use:
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E-mail to administrators: href=3D"mailto:CHEMISTRY-REQUEST.:.c= > cl.net">CHEMISTRY-REQUEST.:.ccl.net or > use
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Job: href=3D"http://www.ccl.net/jobs">http://www.ccl.net/job= > s
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Search Messages: href=3D"http://www.ccl.net/htdig">http://ww= > w.ccl.net/htdig  (login: ccl, Password: > search)

If you= r mail bounces from CCL with 5.7.1 > error, check:
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-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+-+-= > +-+-+-+-+-+-+-+-+-+-+-+ >

Better check out this site for conversion:

href=3D"http://dasher.wustl.edu/tinker/">http://dasher.wustl.edu/ti= > nker/

On 5/1/06, class=3D"gmail_sendername">J= uan Gil > dagur99[-]hotmail.com < .net">owner-chemistry.:.ccl.net> wrote: >

MARGIN: 0px 0= px 0px 0.8ex; BORDER-LEFT: #ccc 1px > solid">Sent to CCL by: "Juan = Gil" > [dagur99**hotmail.com] r>I'm interested in conversion methods from internal to cartesian > r>coordinat= > es for academic use. Any information is welcome, thanks a lot. >

-=3D This is automatically added to each > message by the mai= ling script =3D-
To recover the email > address of the author of the messa= ge, please change
the > strange characters on the top line to the .:. sign. = You can > also
E-mail to = > subscribers: href=3D"mailto:CHEMISTRY.:.ccl.net">CHEMISTRY.:.ccl.net > or = use:
     href=3D"http://www.ccl.net/cgi-bin/ccl/= > send_ccl_message">http://www.ccl.net/cgi-bin/ccl/send_ccl_message >

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Job: href=3D"http://www.ccl.net/jobs">http://www.ccl.net/job= > s
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clear=3D"all">
--
Neeraj = Misra PhD
Assoc.Prof in > Physics
Lucknow University 226007
Phone 05= 22-2740410 > (O)
&nb= > sp; 0522-3253647 (R)
Cell # 9335333805=20 > > ------=_Part_13309_23377682.1146447691018-- > > > > -= This is automatically added to each message by the mailing > script =- To recover the email address of the author of the > message, please change the strange characters on the top line > to the ## sign. You can also look up the X-Original-From: line > in the mail header.> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, > Password: search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+ > > > > > > From owner-chemistry@ccl.net Mon May 1 13:55:00 2006 From: "Igor Filippov Contr igorf++helix.nih.gov" To: CCL Subject: CCL: help needed Message-Id: <-31645-060501123015-9388-y5b7V/ULBD9myz8aGrzN/g**server.ccl.net> X-Original-From: "Igor Filippov [Contr]" Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Mon, 01 May 2006 11:03:03 -0400 Mime-Version: 1.0 Sent to CCL by: "Igor Filippov [Contr]" [igorf||helix.nih.gov] A 5 line perl script would do that in no time at all. It will take 5 minutes to write a script and another 5 to run it, why waste time with spreadsheet programs and **shudder** MS-Word ??? Igor On Mon, 2006-05-01 at 10:31 -0400, Jozsef Csontos jozsefcsontos_- _creighton.edu wrote: > Sent to CCL by: Jozsef Csontos [jozsefcsontos{}creighton.edu] > Hi, > > I can imagine that gnumeric doesn't have this "excel" limitation, but > I'm not sure, so why don't you check it. It has ported to windows, too. > > Good luck, > > Jozsef > On Mon, 2006-05-01 at 08:34 -0400, Richard L. Wood rwoodphd:msn.com > wrote: > > Sent to CCL by: "Richard L. Wood" [rwoodphd##msn.com] > > Hi all, > > > > This question isn't a direct computational chemistry question, but an indirect one. So please bear with me. > > > > I'm trying to analyze the output of a 1 nanosecond MD calculation that I ran using the program NAMD. Since it's a text file, I could use MS Excel to open it and sort the energies from lowest to highest value, which is what I would like to do. However, MS Excel has a limit of about 65000 lines of text (or rows) that a file can contain. Mine has 2000000 lines of text, so that my file is too big. My workaround is to open the file in MS Word, and cut it into pieces that can be opened in MS Excel. Then I can find the minimum energy fro each piece, save that value, and then when done, find the overall minimum. Once I've done this, I can find the corresponding frame number in the file that contained it, go to the trajectory and save those coordinates. > > > > However, as you can imagine, this isn't a very efficient process. My simulation takes about 2 and half hours or so to run, while this analysis takes about two hours to do. I can therefore do about one of these in a day, as I have another non-computational "job" that I am doing. At some point, I will be running some smalled calculations, which will take much less than two hours to run, and so the analysis will take longer than the simulation! > > > > My question is this: does anyone know of a spreadsheat program where I can a) import a text file of more than 65000 rows easily, b) can sort a given column of that file, and c) works under Windows and is free? I've tried Quattro Pro, and all the file comes out in a single row! > > > > TIA, > > Richard> > > > > From owner-chemistry@ccl.net Mon May 1 16:06:01 2006 From: "Young Leh youngleh]-[gmail.com" To: CCL Subject: CCL:G: Gaussian Error: NtrErr Called from FileIO Message-Id: <-31646-060501160508-11111-iJRNte2HhoJXWUgsgC0Luw * server.ccl.net> X-Original-From: "Young Leh" Date: Mon, 1 May 2006 16:05:06 -0400 Sent to CCL by: "Young Leh" [youngleh---gmail.com] Dear CCLer, I ran into the Gaussian error on a simple calculaton of CuO with B3LYP/LANL2DZ. Does anybody know what error this is? dumping /fiocom/, unit = 3 NFiles = 1 SizExt = 524288 WInBlk = 512 defal = T LstWrd = 65536 FType=2 FMxFil=10000 Number 0 Base 20480 End 65536 End1 65536 Wr Pntr 20480 Rd Pntr 20480 Length 45056 Error termination in NtrErr: NtrErr Called from FileIO. Sincerely, Youngleh From owner-chemistry@ccl.net Mon May 1 20:35:01 2006 From: "RICHARD JILL WOOD rwoodphd++msn.com" To: CCL Subject: CCL: help needed Message-Id: <-31647-060501103227-31021-1dQNvUFPoxi2TC/DAAuBqg*server.ccl.net> X-Original-From: "RICHARD JILL WOOD" Content-Type: text/plain; format=flowed Date: Mon, 01 May 2006 13:45:09 +0000 Mime-Version: 1.0 Sent to CCL by: "RICHARD JILL WOOD" [rwoodphd+*+msn.com] Hi Serena: Not to sound lazy, but the problem is that I just don't have the "spare time" to write code, in unix, or any other language. I work five days a week at a low paying non-computational chemistry job, and I have two days off to work on this project (which I'm not getting compensated for, obviously) a week, and I'd like to be spending my free time working on the project, as opposed to writing code for it. I'm hoping to get this data, package it together with some other calculations that I did when I was a professional computational chemist, and publish it. Obviously, I'm also looking for another computational chemist position. So, I'd appreciate any help you can offer. Richard >From: "Serena Povia sp422]|[hermes.cam.ac.uk" >Reply-To: "CCL Subscribers" >To: "Wood, Richard L. " >Subject: CCL: help needed >Date: Mon, 1 May 2006 09:11:09 -0400 > >Sent to CCL by: Serena Povia [sp422(_)hermes.cam.ac.uk] >Dear Rich, > >I'm sorry to tell you that your problem could be *easily* solved in >unix, writing a bash/perl script to grep the energy line you're >interested in some way, and sort them, and go back to pick up the >energies. It's really a matter of 50 lines of code at >most and once it's done everything will be authomatic for the following >calculations. > >if you run your calculations on a unix machine you could even run the >analysis script on it an then get your nice data back in windows. I'm >learning bash myself and I'll be happy to help. > >best, serena > > >On Mon, 1 May 2006, Richard L. Wood rwoodphd:msn.com wrote: > > > Sent to CCL by: "Richard L. Wood" [rwoodphd##msn.com] > > Hi all, > > > > This question isn't a direct computational chemistry question, but an >indirect one. So please bear with me. > > > > I'm trying to analyze the output of a 1 nanosecond MD calculation that I >ran using the program NAMD. Since it's a text file, I could use MS Excel >to open it and sort the energies from lowest to highest value, which is >what I would like to do. However, MS Excel has a limit of about 65000 >lines of text (or rows) that a file can contain. Mine has 2000000 lines of >text, so that my file is too big. My workaround is to open the file in MS >Word, and cut it into pieces that can be opened in MS Excel. Then I can >find the minimum energy fro each piece, save that value, and then when >done, find the overall minimum. Once I've done this, I can find the >corresponding frame number in the file that contained it, go to the >trajectory and save those coordinates. > > > > However, as you can imagine, this isn't a very efficient process. My >simulation takes about 2 and half hours or so to run, while this analysis >takes about two hours to do. I can therefore do about one of these in a >day, as I have another non-computational "job" that I am doing. At some >point, I will be running some smalled calculations, which will take much >less than two hours to run, and so the analysis will take longer than the >simulation! > > > > My question is this: does anyone know of a spreadsheat program where I >can a) import a text file of more than 65000 rows easily, b) can sort a >given column of that file, and c) works under Windows and is free? I've >tried Quattro Pro, and all the file comes out in a single row! > > > > TIA, > > Richard> > > _________________________________________________________________ Express yourself instantly with MSN Messenger! Download today - it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/