From owner-chemistry@ccl.net Fri Aug 12 03:15:00 2011 From: "Hanjo Kim lordmiss]^[gmail.com" To: CCL Subject: CCL: models to predict small molecule fluorescence, publications? Message-Id: <-45244-110812031317-12595-Ptl2tobLuBvaufR1Y79Dhw++server.ccl.net> X-Original-From: Hanjo Kim Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 12 Aug 2011 15:13:10 +0800 MIME-Version: 1.0 Sent to CCL by: Hanjo Kim [lordmiss++gmail.com] Here is one paper from my group. Quantitative structure-fluorescence property relationship analysis of a large BODIPY library, Schueller, A.; Goh, G. B.; Kim, H.; Lee, J. S.; Chang, Y. T. Mol. Inf., 2010, 29, 717-729. Regards, http://lordmiss.com http://agile2robust.com 2011/8/11 James Thomas Metz James.Metz^_^Abbott.com : > > Sent to CCL by: "James Thomas Metz" [James.Metz+/-Abbott.com] > CCL, > > Can someone direct me to any publications describing models to predict small molecule fluorescence using cheminformatics-type approaches i.e., pattern recognition of aromatic rings or substructures which have a high probability > of fluorescence. > > I am trying to avoid QM or semi-empirical approaches, if possible. > > Alternatively, if someone is aware of databases of compounds which have been > tested for fluorescence and contain positives and negatives that would be excellent.  I have access to software that would allow me to construct in-house > models given enough quality data. > > Thank you. > > Regards, > Jim Metz > Abbott Laboratories>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > > From owner-chemistry@ccl.net Fri Aug 12 08:06:00 2011 From: "Andrew Orry andy:molsoft.com" To: CCL Subject: CCL: MolSoft ICM Workshop - Protein Structure and Drug Design Message-Id: <-45245-110811233025-8115-kdOibE7B+4aZZ2b5t0su8w.@.server.ccl.net> X-Original-From: Andrew Orry Content-Type: multipart/alternative; boundary="------------020003030905060306070008" Date: Thu, 11 Aug 2011 18:18:07 -0700 MIME-Version: 1.0 Sent to CCL by: Andrew Orry [andy.|.molsoft.com] This is a multi-part message in MIME format. --------------020003030905060306070008 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Please join us at the next MolSoft ICM Workshop - *Protein Structure and Drug Design*. *September 29th-30th 2011, San Diego, CA* Click here for more information and a registration form. Price: Academics = $399 ($349 before 8/29/11) Commercial = $799 ($749 before 8/29/11) The workshop is suitable for chemists and biologists who would like to learn more about computational drug discovery, molecular modeling, and bioinformatics. No prior knowledge in this field is required to participate in this workshop. The workshop will consist of lectures, demonstrations, and "hands-on" experiments covering the following topics: * Molecular Graphics and Displaying Interactive Molecules in PowerPoint and the Web using ActiveICM . * Sequence and Protein Structure Analysis. * Protein Modeling and Simulations. * Structure Validation and Optimization. * Ligand Binding Site Prediction. * Protein-Protein Docking. * Small Molecule Docking and Virtual Ligand Screening . * ICM 3D Interactive Ligand Editor . * Structure-based development of target-specific compound libraries . * Cheminformatics : chemical clustering, searching, superposition etc... * QSAR The workshop is presented by: Ruben Abagyan - Professor, University of California San Diego Max Totrov - Principal Scientist, MolSoft LLC Andrew Orry - Senior Research Scientist, MolSoft LLC Follow us on: Facebook Twitter Youtube --------------020003030905060306070008 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Please join us at the next MolSoft ICM Workshop - Protein Structure and Drug Design.

September 29th-30th 2011, San Diego, CA

Click here for more information and a registration form.

Price:
Academics =   $399 ($349 before 8/29/11)
Commercial = $799 ($749 before 8/29/11)

The workshop is suitable for chemists and biologists who would like to learn more about computational drug discovery, molecular modeling, and bioinformatics. No prior knowledge in this field is required to participate in this workshop. The workshop will consist of lectures, demonstrations, and "hands-on" experiments covering the following topics:
  • Molecular Graphics and Displaying Interactive Molecules in PowerPoint and the Web using ActiveICM.
  • Sequence and Protein Structure Analysis.
  • Protein Modeling and Simulations.
  • Structure Validation and Optimization.
  • Ligand Binding Site Prediction.
  • Protein-Protein Docking.
  • Small Molecule Docking and Virtual Ligand Screening.
  • ICM 3D Interactive Ligand Editor.
  • Structure-based development of target-specific compound libraries.
  • Cheminformatics: chemical clustering, searching, superposition etc...
  • QSAR                                                                                            
The workshop is presented by:
Ruben Abagyan - Professor, University of California San Diego
Max Totrov - Principal Scientist, MolSoft LLC
Andrew Orry - Senior Research Scientist, MolSoft LLC

Follow us on:
Facebook
Twitter
Youtube

--------------020003030905060306070008-- From owner-chemistry@ccl.net Fri Aug 12 14:31:00 2011 From: "Richard Leo Wood rwoodphd||msn.com" To: CCL Subject: CCL: Fortran question Message-Id: <-45246-110812142946-5079-/vR4robuXdGjEygBcI0W0Q.@.server.ccl.net> X-Original-From: "Richard Leo Wood" Date: Fri, 12 Aug 2011 14:29:42 -0400 Sent to CCL by: "Richard Leo Wood" [rwoodphd(_)msn.com] Hi all, I have a real simple Fortran question-however, I cna't seem to find the answer anywhere and I've looked everywhere. I'm trying to write a Fortran program that will read in an external molecule file in dat format, manipulate it and then write the output to a new dat file. I'm at the point where I am reading in the file and trying to write it out. Here's my file: 00012 benzene 002 00002 2 00006 1 00007 1 00000 0 00000 0 00000 0 -000.696800 -001.210000 -000.001000 0 10 000.00000000.00000 002 00001 2 00003 1 00008 1 00000 0 00000 0 00000 0 0000.699600 -001.208900 0000.000000 0 10 000.00000000.00000 002 00002 1 00004 2 00009 1 00000 0 00000 0 00000 0 0001.396500 0000.001200 0000.001000 0 10 000.00000000.00000 002 00003 2 00005 1 00010 1 00000 0 00000 0 00000 0 0000.697000 0001.209900 0000.001000 0 10 000.00000000.00000 002 00004 1 00006 2 00011 1 00000 0 00000 0 00000 0 -000.699400 0001.208600 0000.000000 0 10 000.00000000.00000 002 00001 1 00005 2 00012 1 00000 0 00000 0 00000 0 -001.396500 -000.001400 -000.001000 0 10 000.00000000.00000 041 00001 1 00000 0 00000 0 00000 0 00000 0 00000 0 -001.247600 -002.165800 -000.001800 0 21 000.00000000.00000 041 00002 1 00000 0 00000 0 00000 0 00000 0 00000 0 0001.252000 -002.163700 0000.000000 0 21 000.00000000.00000 041 00003 1 00000 0 00000 0 00000 0 00000 0 00000 0 0002.499600 0000.002400 0000.001800 0 21 000.00000000.00000 041 00004 1 00000 0 00000 0 00000 0 00000 0 00000 0 0001.247700 0002.165800 0000.001800 0 21 000.00000000.00000 041 00005 1 00000 0 00000 0 00000 0 00000 0 00000 0 -001.252000 0002.163400 0000.000000 0 21 000.00000000.00000 041 00006 1 00000 0 00000 0 00000 0 00000 0 00000 0 -002.499600 -000.002600 -000.001800 0 21 000.00000000.00000 I read it in, and when I write it out to a new file, all I get is the 00012. So, that's all it is reading in or all it is writing out. How can I get my code to read the whole molecule in and then write it all back out? TIA. From owner-chemistry@ccl.net Fri Aug 12 15:47:00 2011 From: "Ahmed E. Ismail aei=alum.mit.edu" To: CCL Subject: CCL: Fortran question Message-Id: <-45247-110812150309-8928-LHMEcshjAE91Fd4PhkU8DA()server.ccl.net> X-Original-From: "Ahmed E. Ismail" Content-Type: multipart/alternative; boundary=001636e0a6ead1a23204aa538f60 Date: Fri, 12 Aug 2011 21:02:58 +0200 MIME-Version: 1.0 Sent to CCL by: "Ahmed E. Ismail" [aei/a\alum.mit.edu] --001636e0a6ead1a23204aa538f60 Content-Type: text/plain; charset=windows-1252 Content-Transfer-Encoding: quoted-printable It's very hard for us to answer a question like that when you don't show us what code you used to read in the file, and what you used to output it. it might be an issue with your formatting command=97you've set up a loop condition that fails immediately, preventing anything from being written. O= r there's a thousand other possibilities. But reading and writing data in Fortran isn't too hard, if you know the format of the data. =97AEI On 12 August 2011 20:29, Richard Leo Wood rwoodphd||msn.com < owner-chemistry!=!ccl.net> wrote: > > Sent to CCL by: "Richard Leo Wood" [rwoodphd(_)msn.com] > Hi all, > > I have a real simple Fortran question-however, I cna't seem to find the > answer anywhere and I've looked everywhere. > > I'm trying to write a Fortran program that will read in an external > molecule file in dat format, manipulate it and then write the output to a > new dat file. > > I'm at the point where I am reading in the file and trying to write it ou= t. > > Here's my file: > > 00012 benzene > 002 00002 2 00006 1 00007 1 00000 0 00000 0 00000 0 -000.696800 > -001.210000 -000.001000 0 10 000.00000000.00000 > 002 00001 2 00003 1 00008 1 00000 0 00000 0 00000 0 0000.699600 > -001.208900 0000.000000 0 10 000.00000000.00000 > 002 00002 1 00004 2 00009 1 00000 0 00000 0 00000 0 0001.396500 > 0000.001200 0000.001000 0 10 000.00000000.00000 > 002 00003 2 00005 1 00010 1 00000 0 00000 0 00000 0 0000.697000 > 0001.209900 0000.001000 0 10 000.00000000.00000 > 002 00004 1 00006 2 00011 1 00000 0 00000 0 00000 0 -000.699400 > 0001.208600 0000.000000 0 10 000.00000000.00000 > 002 00001 1 00005 2 00012 1 00000 0 00000 0 00000 0 -001.396500 > -000.001400 -000.001000 0 10 000.00000000.00000 > 041 00001 1 00000 0 00000 0 00000 0 00000 0 00000 0 -001.247600 > -002.165800 -000.001800 0 21 000.00000000.00000 > 041 00002 1 00000 0 00000 0 00000 0 00000 0 00000 0 0001.252000 > -002.163700 0000.000000 0 21 000.00000000.00000 > 041 00003 1 00000 0 00000 0 00000 0 00000 0 00000 0 0002.499600 > 0000.002400 0000.001800 0 21 000.00000000.00000 > 041 00004 1 00000 0 00000 0 00000 0 00000 0 00000 0 0001.247700 > 0002.165800 0000.001800 0 21 000.00000000.00000 > 041 00005 1 00000 0 00000 0 00000 0 00000 0 00000 0 -001.252000 > 0002.163400 0000.000000 0 21 000.00000000.00000 > 041 00006 1 00000 0 00000 0 00000 0 00000 0 00000 0 -002.499600 > -000.002600 -000.001800 0 21 000.00000000.00000 > > I read it in, and when I write it out to a new file, all I get is the > 00012. > > So, that's all it is reading in or all it is writing out. How can I get = my > code to read the whole molecule in and then write it all back out? > > TIA. > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Ahmed E. Ismail aei!=!alum.mit.edu aei!=!aya.yale.edu --001636e0a6ead1a23204aa538f60 Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: quoted-printable It's very hard for us to answer a question like that when you don't= show us what code you used to read in the file, and what you used to outpu= t it. it might be an issue with your formatting command=97you've set up= a loop condition that fails immediately, preventing anything from being wr= itten. Or there's a thousand other possibilities. But reading and writi= ng data in Fortran isn't too hard, if you know the format of the data.<= div>
=97AEI

On 12 August 2011 2= 0:29, Richard Leo Wood rwoodphd||msn.com <owner-chemist= ry!=!ccl.net> wrote:

Sent to CCL by: "Richard Leo Wood" [rwoodphd(_)msn.com]
Hi all,

I have a real simple Fortran question-however, I cna't seem to find the= answer anywhere and I've looked everywhere.

I'm trying to write a Fortran program that will read in an external mol= ecule file in dat format, manipulate it and then write the output to a new = dat file.

I'm at the point where I am reading in the file and trying to write it = out.

Here's my file:

00012 =A0benzene
=A0002 00002 2 00006 1 00007 1 00000 0 00000 0 00000 0 -000.696800 -001.210= 000 -000.001000 0 =A010 =A0 =A0 =A0000.00000000.00000
=A0002 00001 2 00003 1 00008 1 00000 0 00000 0 00000 0 0000.699600 -001.208= 900 0000.000000 0 =A010 =A0 =A0 =A0000.00000000.00000
=A0002 00002 1 00004 2 00009 1 00000 0 00000 0 00000 0 0001.396500 0000.001= 200 0000.001000 0 =A010 =A0 =A0 =A0000.00000000.00000
=A0002 00003 2 00005 1 00010 1 00000 0 00000 0 00000 0 0000.697000 0001.209= 900 0000.001000 0 =A010 =A0 =A0 =A0000.00000000.00000
=A0002 00004 1 00006 2 00011 1 00000 0 00000 0 00000 0 -000.699400 0001.208= 600 0000.000000 0 =A010 =A0 =A0 =A0000.00000000.00000
=A0002 00001 1 00005 2 00012 1 00000 0 00000 0 00000 0 -001.396500 -000.001= 400 -000.001000 0 =A010 =A0 =A0 =A0000.00000000.00000
=A0041 00001 1 00000 0 00000 0 00000 0 00000 0 00000 0 -001.247600 -002.165= 800 -000.001800 0 =A021 =A0 =A0 =A0000.00000000.00000
=A0041 00002 1 00000 0 00000 0 00000 0 00000 0 00000 0 0001.252000 -002.163= 700 0000.000000 0 21 =A0 =A0 =A0 000.00000000.00000
=A0041 00003 1 00000 0 00000 0 00000 0 00000 0 00000 0 0002.499600 0000.002= 400 0000.001800 0 21 =A0 =A0 =A0 000.00000000.00000
=A0041 00004 1 00000 0 00000 0 00000 0 00000 0 00000 0 0001.247700 0002.165= 800 0000.001800 0 21 =A0 =A0 =A0 000.00000000.00000
=A0041 00005 1 00000 0 00000 0 00000 0 00000 0 00000 0 -001.252000 0002.163= 400 0000.000000 0 21 =A0 =A0 =A0 000.00000000.00000
=A0041 00006 1 00000 0 00000 0 00000 0 00000 0 00000 0 -002.499600 -000.002= 600 -000.001800 0 21 =A0 =A0 =A0 000.00000000.00000

I read it in, and when I write it out to a new file, all I get is the 00012= .

So, that's all it is reading in or all it is writing out. =A0How can I = get my code to read the whole molecule in and then write it all back out?
TIA.



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY!=!ccl.n= et or use:
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEM= ISTRY-REQUEST!=!ccl.net or use
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

Subscribe/Unsubscribe:
=A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.n= et/jobs
Conferences: http://server.ccl.net/chemistry/announcements/co= nferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
=A0 =A0 =A0h= ttp://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/





--
=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Ahmed E. Ismailaei!=!alum.mit.edu
aei!=!aya.yale.edu

--001636e0a6ead1a23204aa538f60-- From owner-chemistry@ccl.net Fri Aug 12 16:21:00 2011 From: "Shobana Sundaram/FS/VCU ssundaram*o*vcu.edu" To: CCL Subject: CCL: Fortran question Message-Id: <-45248-110812160356-29850-jbt6CYuR7Vgm6wLysX0uOw.@.server.ccl.net> X-Original-From: Shobana Sundaram/FS/VCU Content-Type: multipart/alternative; boundary="=_alternative 006E2FBF852578EA_=" Date: Fri, 12 Aug 2011 16:03:46 -0400 MIME-Version: 1.0 Sent to CCL by: Shobana Sundaram/FS/VCU [ssundaram()vcu.edu] This is a multipart message in MIME format. --=_alternative 006E2FBF852578EA_= Content-Type: text/plain; charset="US-ASCII" Hi, It would be nice to see your code as well. Nevertheless, you may not have assigned the second variable that reads 'benzene' as character. Most Fortran codes would terminate writing at that point. Also most Fortran compilers by default ignore anything past the 80th column position in a line. However, this can be over-ridden by compiler options Good Luck! -shobana --------------- Shobana Sundaram, Ph.D., Instructor, VCU-SOM, Richmond, VA > From: "Richard Leo Wood rwoodphd||msn.com" To: "Sundaram, Shobana " Date: 08/12/2011 03:06 PM Subject: CCL: Fortran question Sent by: owner-chemistry+ssundaram==vcu.edu:+:ccl.net Sent to CCL by: "Richard Leo Wood" [rwoodphd(_)msn.com] Hi all, I have a real simple Fortran question-however, I cna't seem to find the answer anywhere and I've looked everywhere. I'm trying to write a Fortran program that will read in an external molecule file in dat format, manipulate it and then write the output to a new dat file. I'm at the point where I am reading in the file and trying to write it out. Here's my file: 00012 benzene 002 00002 2 00006 1 00007 1 00000 0 00000 0 00000 0 -000.696800 -001.210000 -000.001000 0 10 000.00000000.00000 002 00001 2 00003 1 00008 1 00000 0 00000 0 00000 0 0000.699600 -001.208900 0000.000000 0 10 000.00000000.00000 002 00002 1 00004 2 00009 1 00000 0 00000 0 00000 0 0001.396500 0000.001200 0000.001000 0 10 000.00000000.00000 002 00003 2 00005 1 00010 1 00000 0 00000 0 00000 0 0000.697000 0001.209900 0000.001000 0 10 000.00000000.00000 002 00004 1 00006 2 00011 1 00000 0 00000 0 00000 0 -000.699400 0001.208600 0000.000000 0 10 000.00000000.00000 002 00001 1 00005 2 00012 1 00000 0 00000 0 00000 0 -001.396500 -000.001400 -000.001000 0 10 000.00000000.00000 041 00001 1 00000 0 00000 0 00000 0 00000 0 00000 0 -001.247600 -002.165800 -000.001800 0 21 000.00000000.00000 041 00002 1 00000 0 00000 0 00000 0 00000 0 00000 0 0001.252000 -002.163700 0000.000000 0 21 000.00000000.00000 041 00003 1 00000 0 00000 0 00000 0 00000 0 00000 0 0002.499600 0000.002400 0000.001800 0 21 000.00000000.00000 041 00004 1 00000 0 00000 0 00000 0 00000 0 00000 0 0001.247700 0002.165800 0000.001800 0 21 000.00000000.00000 041 00005 1 00000 0 00000 0 00000 0 00000 0 00000 0 -001.252000 0002.163400 0000.000000 0 21 000.00000000.00000 041 00006 1 00000 0 00000 0 00000 0 00000 0 00000 0 -002.499600 -000.002600 -000.001800 0 21 000.00000000.00000 I read it in, and when I write it out to a new file, all I get is the 00012. So, that's all it is reading in or all it is writing out. How can I get my code to read the whole molecule in and then write it all back out? TIA.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--=_alternative 006E2FBF852578EA_= Content-Type: text/html; charset="US-ASCII" Hi,

It would be nice to see your code as well. Nevertheless, you may not have assigned the second variable that reads 'benzene' as character.  Most Fortran codes would terminate writing at that point.  Also  most Fortran compilers by default ignore anything past the 80th column position in a line. However, this can be over-ridden by compiler options

Good Luck!

-shobana

---------------
Shobana Sundaram, Ph.D.,
Instructor,
VCU-SOM,
Richmond, VA



From:        "Richard Leo Wood rwoodphd||msn.com" <owner-chemistry:+:ccl.net>
To:        "Sundaram, Shobana " <ssundaram:+:vcu.edu>
Date:        08/12/2011 03:06 PM
Subject:        CCL: Fortran question
Sent by:        owner-chemistry+ssundaram==vcu.edu:+:ccl.net




Sent to CCL by: "Richard Leo Wood" [rwoodphd(_)msn.com]
Hi all,

I have a real simple Fortran question-however, I cna't seem to find the answer anywhere and I've looked everywhere.

I'm trying to write a Fortran program that will read in an external molecule file in dat format, manipulate it and then write the output to a new dat file.

I'm at the point where I am reading in the file and trying to write it out.

Here's my file:

00012  benzene
002 00002 2 00006 1 00007 1 00000 0 00000 0 00000 0 -000.696800 -001.210000 -000.001000 0  10      000.00000000.00000
002 00001 2 00003 1 00008 1 00000 0 00000 0 00000 0 0000.699600 -001.208900 0000.000000 0  10      000.00000000.00000
002 00002 1 00004 2 00009 1 00000 0 00000 0 00000 0 0001.396500 0000.001200 0000.001000 0  10      000.00000000.00000
002 00003 2 00005 1 00010 1 00000 0 00000 0 00000 0 0000.697000 0001.209900 0000.001000 0  10      000.00000000.00000
002 00004 1 00006 2 00011 1 00000 0 00000 0 00000 0 -000.699400 0001.208600 0000.000000 0  10      000.00000000.00000
002 00001 1 00005 2 00012 1 00000 0 00000 0 00000 0 -001.396500 -000.001400 -000.001000 0  10      000.00000000.00000
041 00001 1 00000 0 00000 0 00000 0 00000 0 00000 0 -001.247600 -002.165800 -000.001800 0  21      000.00000000.00000
041 00002 1 00000 0 00000 0 00000 0 00000 0 00000 0 0001.252000 -002.163700 0000.000000 0 21       000.00000000.00000
041 00003 1 00000 0 00000 0 00000 0 00000 0 00000 0 0002.499600 0000.002400 0000.001800 0 21       000.00000000.00000
041 00004 1 00000 0 00000 0 00000 0 00000 0 00000 0 0001.247700 0002.165800 0000.001800 0 21       000.00000000.00000
041 00005 1 00000 0 00000 0 00000 0 00000 0 00000 0 -001.252000 0002.163400 0000.000000 0 21       000.00000000.00000
041 00006 1 00000 0 00000 0 00000 0 00000 0 00000 0 -002.499600 -000.002600 -000.001800 0 21       000.00000000.00000

I read it in, and when I write it out to a new file, all I get is the 00012.

So, that's all it is reading in or all it is writing out.  How can I get my code to read the whole molecule in and then write it all back out?

TIA.


     http://www.ccl.net/cgi-bin/ccl/send_ccl_message
     http://www.ccl.net/cgi-bin/ccl/send_ccl_message
     http://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs
Conferences: http://server.ccl.net/chemistry/announcements/conferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
     http://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/
--=_alternative 006E2FBF852578EA_=-- From owner-chemistry@ccl.net Fri Aug 12 16:56:02 2011 From: "Radoslaw Kaminski rkaminski.rk^-^gmail.com" To: CCL Subject: CCL: Fortran question Message-Id: <-45249-110812160425-30199-G8zJQe1fF5fM8it41CrSKg .. server.ccl.net> X-Original-From: Radoslaw Kaminski Content-Type: multipart/alternative; boundary=0016361e7ae005108b04aa546bf1 Date: Fri, 12 Aug 2011 22:04:16 +0200 MIME-Version: 1.0 Sent to CCL by: Radoslaw Kaminski [rkaminski.rk^gmail.com] --0016361e7ae005108b04aa546bf1 Content-Type: text/plain; charset=ISO-8859-1 Hi, Your code would be useful to tell what is wrong:) Radek 2011/8/12 Richard Leo Wood rwoodphd||msn.com > > Sent to CCL by: "Richard Leo Wood" [rwoodphd(_)msn.com] > Hi all, > > I have a real simple Fortran question-however, I cna't seem to find the > answer anywhere and I've looked everywhere. > > I'm trying to write a Fortran program that will read in an external > molecule file in dat format, manipulate it and then write the output to a > new dat file. > > I'm at the point where I am reading in the file and trying to write it out. > > Here's my file: > > 00012 benzene > 002 00002 2 00006 1 00007 1 00000 0 00000 0 00000 0 -000.696800 > -001.210000 -000.001000 0 10 000.00000000.00000 > 002 00001 2 00003 1 00008 1 00000 0 00000 0 00000 0 0000.699600 > -001.208900 0000.000000 0 10 000.00000000.00000 > 002 00002 1 00004 2 00009 1 00000 0 00000 0 00000 0 0001.396500 > 0000.001200 0000.001000 0 10 000.00000000.00000 > 002 00003 2 00005 1 00010 1 00000 0 00000 0 00000 0 0000.697000 > 0001.209900 0000.001000 0 10 000.00000000.00000 > 002 00004 1 00006 2 00011 1 00000 0 00000 0 00000 0 -000.699400 > 0001.208600 0000.000000 0 10 000.00000000.00000 > 002 00001 1 00005 2 00012 1 00000 0 00000 0 00000 0 -001.396500 > -000.001400 -000.001000 0 10 000.00000000.00000 > 041 00001 1 00000 0 00000 0 00000 0 00000 0 00000 0 -001.247600 > -002.165800 -000.001800 0 21 000.00000000.00000 > 041 00002 1 00000 0 00000 0 00000 0 00000 0 00000 0 0001.252000 > -002.163700 0000.000000 0 21 000.00000000.00000 > 041 00003 1 00000 0 00000 0 00000 0 00000 0 00000 0 0002.499600 > 0000.002400 0000.001800 0 21 000.00000000.00000 > 041 00004 1 00000 0 00000 0 00000 0 00000 0 00000 0 0001.247700 > 0002.165800 0000.001800 0 21 000.00000000.00000 > 041 00005 1 00000 0 00000 0 00000 0 00000 0 00000 0 -001.252000 > 0002.163400 0000.000000 0 21 000.00000000.00000 > 041 00006 1 00000 0 00000 0 00000 0 00000 0 00000 0 -002.499600 > -000.002600 -000.001800 0 21 000.00000000.00000 > > I read it in, and when I write it out to a new file, all I get is the > 00012. > > So, that's all it is reading in or all it is writing out. How can I get my > code to read the whole molecule in and then write it all back out? > > TIA.> > > -- Radoslaw Kaminski, M.Sc. Eng. Ph.D. Student Crystallochemistry Laboratory Department of Chemistry University of Warsaw Pasteura 1, 02-093 Warszawa, Poland http://www.chem.uw.edu.pl/people/RKaminski/ --0016361e7ae005108b04aa546bf1 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi,

Your code would be useful to tell what is wrong:)

Radek


2011/8/12 Richard Leo Wood rwoodphd||msn= .com <o= wner-chemistry=ccl.net>

Sent to CCL by: "Richard Leo Wood" [rwoodphd(_)msn.com]
Hi all,

I have a real simple Fortran question-however, I cna't seem to find the= answer anywhere and I've looked everywhere.

I'm trying to write a Fortran program that will read in an external mol= ecule file in dat format, manipulate it and then write the output to a new = dat file.

I'm at the point where I am reading in the file and trying to write it = out.

Here's my file:

00012 =A0benzene
=A0002 00002 2 00006 1 00007 1 00000 0 00000 0 00000 0 -000.696800 -001.210= 000 -000.001000 0 =A010 =A0 =A0 =A0000.00000000.00000
=A0002 00001 2 00003 1 00008 1 00000 0 00000 0 00000 0 0000.699600 -001.208= 900 0000.000000 0 =A010 =A0 =A0 =A0000.00000000.00000
=A0002 00002 1 00004 2 00009 1 00000 0 00000 0 00000 0 0001.396500 0000.001= 200 0000.001000 0 =A010 =A0 =A0 =A0000.00000000.00000
=A0002 00003 2 00005 1 00010 1 00000 0 00000 0 00000 0 0000.697000 0001.209= 900 0000.001000 0 =A010 =A0 =A0 =A0000.00000000.00000
=A0002 00004 1 00006 2 00011 1 00000 0 00000 0 00000 0 -000.699400 0001.208= 600 0000.000000 0 =A010 =A0 =A0 =A0000.00000000.00000
=A0002 00001 1 00005 2 00012 1 00000 0 00000 0 00000 0 -001.396500 -000.001= 400 -000.001000 0 =A010 =A0 =A0 =A0000.00000000.00000
=A0041 00001 1 00000 0 00000 0 00000 0 00000 0 00000 0 -001.247600 -002.165= 800 -000.001800 0 =A021 =A0 =A0 =A0000.00000000.00000
=A0041 00002 1 00000 0 00000 0 00000 0 00000 0 00000 0 0001.252000 -002.163= 700 0000.000000 0 21 =A0 =A0 =A0 000.00000000.00000
=A0041 00003 1 00000 0 00000 0 00000 0 00000 0 00000 0 0002.499600 0000.002= 400 0000.001800 0 21 =A0 =A0 =A0 000.00000000.00000
=A0041 00004 1 00000 0 00000 0 00000 0 00000 0 00000 0 0001.247700 0002.165= 800 0000.001800 0 21 =A0 =A0 =A0 000.00000000.00000
=A0041 00005 1 00000 0 00000 0 00000 0 00000 0 00000 0 -001.252000 0002.163= 400 0000.000000 0 21 =A0 =A0 =A0 000.00000000.00000
=A0041 00006 1 00000 0 00000 0 00000 0 00000 0 00000 0 -002.499600 -000.002= 600 -000.001800 0 21 =A0 =A0 =A0 000.00000000.00000

I read it in, and when I write it out to a new file, all I get is the 00012= .

So, that's all it is reading in or all it is writing out. =A0How can I = get my code to read the whole molecule in and then write it all back out?
TIA.



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY=ccl.n= et or use:
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEM= ISTRY-REQUEST=ccl.net or use
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

Subscribe/Unsubscribe:
=A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.n= et/jobs
Conferences: http://server.ccl.net/chemistry/announcements/co= nferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
=A0 =A0 =A0h= ttp://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/





--
Radoslaw Kaminski, M.Sc= . Eng.
Ph.D. Student
Crystallochemistry Laboratory
Department of C= hemistry
University of Warsaw
Pasteura 1, 02-093 Warszawa, Poland
h= ttp://www.chem.uw.edu.pl/people/RKaminski/
--0016361e7ae005108b04aa546bf1-- From owner-chemistry@ccl.net Fri Aug 12 17:31:00 2011 From: "Close, David M. CLOSED:mail.etsu.edu" To: CCL Subject: CCL: Fortran question Message-Id: <-45250-110812170137-9084-QhgOWzbkhsGzNuVJOPltqw,+,server.ccl.net> X-Original-From: "Close, David M." Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_9D6140C35ABD534F9C463F41FC3A9CC14654FEADetsums2etsuedu_" Date: Fri, 12 Aug 2011 21:01:12 +0000 MIME-Version: 1.0 Sent to CCL by: "Close, David M." [CLOSED%a%mail.etsu.edu] --_000_9D6140C35ABD534F9C463F41FC3A9CC14654FEADetsums2etsuedu_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Ahmed: It is not too easy to answer this question because you do provide the for= mat of these data, and you don't show us the code you have written to attem= pt read/write of these data. We need to know if this is free format or fi= xed format. You say the output stops on the word benzene. This suggests t= hat you are trying to write a character (letter) into a variable (number) f= ormat. If so, this can't be done. Regards, Dave Close. > From: owner-chemistry+closed=3D=3Detsu.edu===ccl.net [mailto:owner-chemistry+= closed=3D=3Detsu.edu===ccl.net] On Behalf Of Ahmed E. Ismail aei=3Dalum.mit.e= du Sent: Friday, August 12, 2011 3:03 PM To: Close, David M. Subject: CCL: Fortran question It's very hard for us to answer a question like that when you don't show us= what code you used to read in the file, and what you used to output it. it= might be an issue with your formatting command-you've set up a loop condit= ion that fails immediately, preventing anything from being written. Or ther= e's a thousand other possibilities. But reading and writing data in Fortran= isn't too hard, if you know the format of the data. -AEI On 12 August 2011 20:29, Richard Leo Wood rwoodphd||msn.com= > wrote: Sent to CCL by: "Richard Leo Wood" [rwoodphd(_)msn.com] Hi all, I have a real simple Fortran question-however, I cna't seem to find the ans= wer anywhere and I've looked everywhere. I'm trying to write a Fortran program that will read in an external molecul= e file in dat format, manipulate it and then write the output to a new dat = file. I'm at the point where I am reading in the file and trying to write it out. Here's my file: 00012 benzene 002 00002 2 00006 1 00007 1 00000 0 00000 0 00000 0 -000.696800 -001.21000= 0 -000.001000 0 10 000.00000000.00000 002 00001 2 00003 1 00008 1 00000 0 00000 0 00000 0 0000.699600 -001.20890= 0 0000.000000 0 10 000.00000000.00000 002 00002 1 00004 2 00009 1 00000 0 00000 0 00000 0 0001.396500 0000.00120= 0 0000.001000 0 10 000.00000000.00000 002 00003 2 00005 1 00010 1 00000 0 00000 0 00000 0 0000.697000 0001.20990= 0 0000.001000 0 10 000.00000000.00000 002 00004 1 00006 2 00011 1 00000 0 00000 0 00000 0 -000.699400 0001.20860= 0 0000.000000 0 10 000.00000000.00000 002 00001 1 00005 2 00012 1 00000 0 00000 0 00000 0 -001.396500 -000.00140= 0 -000.001000 0 10 000.00000000.00000 041 00001 1 00000 0 00000 0 00000 0 00000 0 00000 0 -001.247600 -002.16580= 0 -000.001800 0 21 000.00000000.00000 041 00002 1 00000 0 00000 0 00000 0 00000 0 00000 0 0001.252000 -002.16370= 0 0000.000000 0 21 000.00000000.00000 041 00003 1 00000 0 00000 0 00000 0 00000 0 00000 0 0002.499600 0000.00240= 0 0000.001800 0 21 000.00000000.00000 041 00004 1 00000 0 00000 0 00000 0 00000 0 00000 0 0001.247700 0002.16580= 0 0000.001800 0 21 000.00000000.00000 041 00005 1 00000 0 00000 0 00000 0 00000 0 00000 0 -001.252000 0002.16340= 0 0000.000000 0 21 000.00000000.00000 041 00006 1 00000 0 00000 0 00000 0 00000 0 00000 0 -002.499600 -000.00260= 0 -000.001800 0 21 000.00000000.00000 I read it in, and when I write it out to a new file, all I get is the 00012= . So, that's all it is reading in or all it is writing out. How can I get my= code to read the whole molecule in and then write it all back out? TIA. -=3D This is automatically added to each message by the mailing script =3D-=
or u= se:E-mail to administrators: CHEMISTRY-REQUEST|*|ccl.net or usehttp://www.ccl.net/chemistry/sub_unsub.shtml aei|*|aya.yale.edu --_000_9D6140C35ABD534F9C463F41FC3A9CC14654FEADetsums2etsuedu_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Ahmed:

  It is not too easy to= answer this question because you do provide the format of these data, and = you don’t show us the code you have written to attempt read/write of =  these data.  We need to know if this is free format or fixed for= mat.  You say the output stops on the word benzene.  This suggest= s that you are trying to write a character (letter) into a variable (number= ) format.  If so, this can’t be done. 

  Regards, Dave Close.

From: owner-chemistry+closed=3D=3Detsu= .edu===ccl.net [mailto:owner-chemistry+closed=3D=3Detsu.edu===ccl.net] On Be= half Of Ahmed E. Ismail aei=3Dalum.mit.edu
Sent: Friday, Augu= st 12, 2011 3:03 PM
To: Close, David M.
Subject: CCL: F= ortran question

 =

It's very hard for us to answer a question l= ike that when you don't show us what code you used to read in the file, and= what you used to output it. it might be an issue with your formatting comm= and—you've set up a loop condition that fails immediately, preventing= anything from being written. Or there's a thousand other possibilities. Bu= t reading and writing data in Fortran isn't too hard, if you know the forma= t of the data.

 

—AEI<= o:p>

On 12 August 2011 20:29, Richard Le= o Wood rwoodphd||msn.com <owner-chemistry|*|ccl.net> wrote:=


Sent to C= CL by: "Richard Leo Wood" [rwoodphd(_)msn.com]
Hi all,

I have a real simple Fortr= an question-however, I cna't seem to find the answer anywhere and I've look= ed everywhere.

I'm trying to write a Fortran program that will read = in an external molecule file in dat format, manipulate it and then write th= e output to a new dat file.

I'm at the point where I am reading in t= he file and trying to write it out.

Here's my file:

00012 &nb= sp;benzene
 002 00002 2 00006 1 00007 1 00000 0 00000 0 00000 0 -00= 0.696800 -001.210000 -000.001000 0  10      000.0000000= 0.00000
 002 00001 2 00003 1 00008 1 00000 0 00000 0 00000 0 0000.6= 99600 -001.208900 0000.000000 0  10      000.00000000.0= 0000
 002 00002 1 00004 2 00009 1 00000 0 00000 0 00000 0 0001.3965= 00 0000.001200 0000.001000 0  10      000.00000000.0000= 0
 002 00003 2 00005 1 00010 1 00000 0 00000 0 00000 0 0000.697000 = 0001.209900 0000.001000 0  10      000.00000000.00000 002 00004 1 00006 2 00011 1 00000 0 00000 0 00000 0 -000.699400 000= 1.208600 0000.000000 0  10      000.00000000.00000
&= nbsp;002 00001 1 00005 2 00012 1 00000 0 00000 0 00000 0 -001.396500 -000.0= 01400 -000.001000 0  10      000.00000000.00000
&nbs= p;041 00001 1 00000 0 00000 0 00000 0 00000 0 00000 0 -001.247600 -002.1658= 00 -000.001800 0  21      000.00000000.00000
 0= 41 00002 1 00000 0 00000 0 00000 0 00000 0 00000 0 0001.252000 -002.163700 = 0000.000000 0 21       000.00000000.00000
 041 00003= 1 00000 0 00000 0 00000 0 00000 0 00000 0 0002.499600 0000.002400 0000.001= 800 0 21       000.00000000.00000
 041 00004 1 00000= 0 00000 0 00000 0 00000 0 00000 0 0001.247700 0002.165800 0000.001800 0 21=       000.00000000.00000
 041 00005 1 00000 0 00000= 0 00000 0 00000 0 00000 0 -001.252000 0002.163400 0000.000000 0 21   =     000.00000000.00000
 041 00006 1 00000 0 00000 0 00000= 0 00000 0 00000 0 -002.499600 -000.002600 -000.001800 0 21     &= nbsp; 000.00000000.00000

I read it in, and when I write it out to a = new file, all I get is the 00012.

So, that's all it is reading in or= all it is writing out.  How can I get my code to read the whole molec= ule in and then write it all back out?

TIA.



-=3D This= is automatically added to each message by the mailing script =3D-<br

E-mail to subscribers: CHEM= ISTRY|*|ccl.net or use:
     http://www.ccl.net/cg= i-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST|*|ccl.net or use<= br>     http://www.ccl.net/cgi-bin/ccl/send_ccl_message

Subscribe/Unsubscribe:
     http://www.ccl.net/= chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net
Job: http://www.ccl= .net/jobs
Conferences: http://server.ccl.net/chemistry= /announcements/conferences/

Search Messages: http://www.cc= l.net/chemistry/searchccl/index.shtml
<br
     = http://www.cc= l.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/abo= utccl/instructions/




--
=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Ahmed E. Is= mail
aei|*|alum.mit.edu
aei|*|aya.yale.edu

= --_000_9D6140C35ABD534F9C463F41FC3A9CC14654FEADetsums2etsuedu_-- From owner-chemistry@ccl.net Fri Aug 12 18:06:00 2011 From: "Jason Swails swails++qtp.ufl.edu" To: CCL Subject: CCL: Fortran question Message-Id: <-45251-110812171357-20420-EjjkVOMaJJhYl8vZB4KiOw%a%server.ccl.net> X-Original-From: Jason Swails Content-Type: multipart/alternative; boundary=001517401a5885edac04aa556301 Date: Fri, 12 Aug 2011 17:13:45 -0400 MIME-Version: 1.0 Sent to CCL by: Jason Swails [swails::qtp.ufl.edu] --001517401a5885edac04aa556301 Content-Type: text/plain; charset=ISO-8859-1 On Fri, Aug 12, 2011 at 2:29 PM, Richard Leo Wood rwoodphd||msn.com < owner-chemistry..ccl.net> wrote: > > Sent to CCL by: "Richard Leo Wood" [rwoodphd(_)msn.com] > Hi all, > > I have a real simple Fortran question-however, I cna't seem to find the > answer anywhere and I've looked everywhere. > > I'm trying to write a Fortran program that will read in an external > molecule file in dat format, manipulate it and then write the output to a > new dat file. > > I'm at the point where I am reading in the file and trying to write it out. > > Here's my file: > > 00012 benzene > 002 00002 2 00006 1 00007 1 00000 0 00000 0 00000 0 -000.696800 > -001.210000 -000.001000 0 10 000.00000000.00000 > 002 00001 2 00003 1 00008 1 00000 0 00000 0 00000 0 0000.699600 > -001.208900 0000.000000 0 10 000.00000000.00000 > 002 00002 1 00004 2 00009 1 00000 0 00000 0 00000 0 0001.396500 > 0000.001200 0000.001000 0 10 000.00000000.00000 > 002 00003 2 00005 1 00010 1 00000 0 00000 0 00000 0 0000.697000 > 0001.209900 0000.001000 0 10 000.00000000.00000 > 002 00004 1 00006 2 00011 1 00000 0 00000 0 00000 0 -000.699400 > 0001.208600 0000.000000 0 10 000.00000000.00000 > 002 00001 1 00005 2 00012 1 00000 0 00000 0 00000 0 -001.396500 > -000.001400 -000.001000 0 10 000.00000000.00000 > 041 00001 1 00000 0 00000 0 00000 0 00000 0 00000 0 -001.247600 > -002.165800 -000.001800 0 21 000.00000000.00000 > 041 00002 1 00000 0 00000 0 00000 0 00000 0 00000 0 0001.252000 > -002.163700 0000.000000 0 21 000.00000000.00000 > 041 00003 1 00000 0 00000 0 00000 0 00000 0 00000 0 0002.499600 > 0000.002400 0000.001800 0 21 000.00000000.00000 > 041 00004 1 00000 0 00000 0 00000 0 00000 0 00000 0 0001.247700 > 0002.165800 0000.001800 0 21 000.00000000.00000 > 041 00005 1 00000 0 00000 0 00000 0 00000 0 00000 0 -001.252000 > 0002.163400 0000.000000 0 21 000.00000000.00000 > 041 00006 1 00000 0 00000 0 00000 0 00000 0 00000 0 -002.499600 > -000.002600 -000.001800 0 21 000.00000000.00000 > > I read it in, and when I write it out to a new file, all I get is the > 00012. > If you don't post any of the code you're trying, we have no idea where you went wrong. You can try this: read(unit_number, fmt='(i5,a)') my_num_1, molecule_name read(unit_number, fmt='(INSERT FMT HERE)') (my_array_of_data(i), i=1, num_data) You need to figure out what your format is. See this website http://www.cs.mtu.edu/~shene/COURSES/cs201/NOTES/chap05/format.html, for instance, that describes how to construct a fortran format string. In the example I provided, it means a 5-digit integer followed by a string (of arbitrary length). (If the molecule file you're reading was created by a fortran program and you have the source code, the format string used to create it should be in there and will be the same as the one you want to use). Fortran is ideally set up for fixed format parsing if you know the format in advance. As someone who has had to do the occasional free-format parsing in Fortran, I'll attest that it's clunky (especially compared to Python, Perl, or awk). Then you want to write in essentially exactly the same way you read everything in (only use write instead of read, and the unit_number should correspond to your output file). HTH, Jason -- Jason M. Swails Quantum Theory Project, University of Florida Ph.D. Graduate Student 352-392-4032 --001517401a5885edac04aa556301 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

On Fri, A= ug 12, 2011 at 2:29 PM, Richard Leo Wood rwoodphd||msn.com <owner-chemistry..ccl.net> wrote:

Sent to CCL by: "Richard Leo Wood" [rwoodphd(_)msn.com]
Hi all,

I have a real simple Fortran question-however, I cna't seem to find the= answer anywhere and I've looked everywhere.

I'm trying to write a Fortran program that will read in an external mol= ecule file in dat format, manipulate it and then write the output to a new = dat file.

I'm at the point where I am reading in the file and trying to write it = out.

Here's my file:

00012 =A0benzene
=A0002 00002 2 00006 1 00007 1 00000 0 00000 0 00000 0 -000.696800 -001.210= 000 -000.001000 0 =A010 =A0 =A0 =A0000.00000000.00000
=A0002 00001 2 00003 1 00008 1 00000 0 00000 0 00000 0 0000.699600 -001.208= 900 0000.000000 0 =A010 =A0 =A0 =A0000.00000000.00000
=A0002 00002 1 00004 2 00009 1 00000 0 00000 0 00000 0 0001.396500 0000.001= 200 0000.001000 0 =A010 =A0 =A0 =A0000.00000000.00000
=A0002 00003 2 00005 1 00010 1 00000 0 00000 0 00000 0 0000.697000 0001.209= 900 0000.001000 0 =A010 =A0 =A0 =A0000.00000000.00000
=A0002 00004 1 00006 2 00011 1 00000 0 00000 0 00000 0 -000.699400 0001.208= 600 0000.000000 0 =A010 =A0 =A0 =A0000.00000000.00000
=A0002 00001 1 00005 2 00012 1 00000 0 00000 0 00000 0 -001.396500 -000.001= 400 -000.001000 0 =A010 =A0 =A0 =A0000.00000000.00000
=A0041 00001 1 00000 0 00000 0 00000 0 00000 0 00000 0 -001.247600 -002.165= 800 -000.001800 0 =A021 =A0 =A0 =A0000.00000000.00000
=A0041 00002 1 00000 0 00000 0 00000 0 00000 0 00000 0 0001.252000 -002.163= 700 0000.000000 0 21 =A0 =A0 =A0 000.00000000.00000
=A0041 00003 1 00000 0 00000 0 00000 0 00000 0 00000 0 0002.499600 0000.002= 400 0000.001800 0 21 =A0 =A0 =A0 000.00000000.00000
=A0041 00004 1 00000 0 00000 0 00000 0 00000 0 00000 0 0001.247700 0002.165= 800 0000.001800 0 21 =A0 =A0 =A0 000.00000000.00000
=A0041 00005 1 00000 0 00000 0 00000 0 00000 0 00000 0 -001.252000 0002.163= 400 0000.000000 0 21 =A0 =A0 =A0 000.00000000.00000
=A0041 00006 1 00000 0 00000 0 00000 0 00000 0 00000 0 -002.499600 -000.002= 600 -000.001800 0 21 =A0 =A0 =A0 000.00000000.00000

I read it in, and when I write it out to a new file, all I get is the 00012= .

If you don't post any of the code= you're trying, we have no idea where you went wrong. =A0You can try th= is:

read(unit_number, fmt=3D'(i5,a)') my_num_1, mol= ecule_name
read(unit_number, fmt=3D'(INSERT FMT HERE)') (= my_array_of_data(i), i=3D1, num_data)

You need to = figure out what your format is. =A0See this website http://www.cs.mtu.= edu/~shene/COURSES/cs201/NOTES/chap05/format.html, for instance, that d= escribes how to construct a fortran format string. =A0In the example I prov= ided, it means a 5-digit integer followed by a string (of arbitrary length)= . =A0(If the molecule file you're reading was created by a fortran prog= ram and you have the source code, the format string used to create it shoul= d be in there and will be the same as the one you want to use). =A0Fortran = is ideally set up for fixed format parsing if you know the format in advanc= e. =A0As someone who has had to do the occasional free-format parsing in Fo= rtran, I'll attest that it's clunky (especially compared to Python,= Perl, or awk).

Then you want to write in essentially exactly the same = way you read everything in (only use write instead of read, and the unit_nu= mber should correspond to your output file).

HTH,<= br> Jason

--
Jason M. Swails
Quantum Theory Pr= oject,
University of Florida
Ph.D. Graduate Student
352-392-4032 --001517401a5885edac04aa556301-- From owner-chemistry@ccl.net Fri Aug 12 19:43:00 2011 From: "steinbrt{:}rci.rutgers.edu" To: CCL Subject: CCL: Fortran question Message-Id: <-45252-110812193356-16866-BeA1W4FUwbFZnUgxItDDeg-.-server.ccl.net> X-Original-From: steinbrt**rci.rutgers.edu Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Fri, 12 Aug 2011 19:33:48 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: steinbrt[-]rci.rutgers.edu Hi, Im not trying to start any flame wars here, but if your goal is manipulation of text files, switching to Perl, Python or some other scripting language should well be worth the initial learning effort. In my opinion, Fortran is about the worst possible choice for writing a small text formating tool unless you are very experienced in it. Admittedly, I do realize this will not help you with the immediate problem at hand... Thomas Dr. Thomas Steinbrecher formerly at the BioMaps Institute Rutgers University 610 Taylor Rd. Piscataway, NJ 08854 From owner-chemistry@ccl.net Fri Aug 12 20:29:01 2011 From: "Van Dam, Hubertus J HubertusJJ.vanDam,,pnnl.gov" To: CCL Subject: CCL: Fortran question Message-Id: <-45253-110812172518-30473-b1R86r3yM/BB4IF25Za4sQ^^^server.ccl.net> X-Original-From: "Van Dam, Hubertus J" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="Windows-1252" Date: Fri, 12 Aug 2011 14:25:06 -0700 MIME-Version: 1.0 Sent to CCL by: "Van Dam, Hubertus J" [HubertusJJ.vanDam]_[pnnl.gov] Hi TIA, I am guessing that you are trying to read in proper numbers. In that case most of your file is OK. However, the last column of every line, from line 2 onwards, reads "000.00000000.00000". This is not a valid number! So if you are trying to read this using free format read statements you will get an I/O error on this and your program will stop. The result of that will be consistent with the result you stated. Your best bet would be to try and use format statements to explain to the code how this weird string should be broken down into two floating point numbers (something like 2f9.5). Alternatively if you have control over whatever generated that file then you might want to adjust the output format so that it prints "000.00000 000.00000" rather than "000.00000000.00000". Probably that will solve your problems and be more easily to read for humans too. Best wishes, Huub ________________________________________ > From: owner-chemistry+hubertus.vandam==pnnl.gov*|*ccl.net [owner-chemistry+hubertus.vandam==pnnl.gov*|*ccl.net] On Behalf Of Ahmed E. Ismail aei=alum.mit.edu [owner-chemistry*|*ccl.net] Sent: Friday, August 12, 2011 12:02 PM To: Van Dam, Hubertus J Subject: CCL: Fortran question It's very hard for us to answer a question like that when you don't show us what code you used to read in the file, and what you used to output it. it might be an issue with your formatting command—you've set up a loop condition that fails immediately, preventing anything from being written. Or there's a thousand other possibilities. But reading and writing data in Fortran isn't too hard, if you know the format of the data. —AEI On 12 August 2011 20:29, Richard Leo Wood rwoodphd||msn.com > wrote: Sent to CCL by: "Richard Leo Wood" [rwoodphd(_)msn.com] Hi all, I have a real simple Fortran question-however, I cna't seem to find the answer anywhere and I've looked everywhere. I'm trying to write a Fortran program that will read in an external molecule file in dat format, manipulate it and then write the output to a new dat file. I'm at the point where I am reading in the file and trying to write it out. Here's my file: 00012 benzene 002 00002 2 00006 1 00007 1 00000 0 00000 0 00000 0 -000.696800 -001.210000 -000.001000 0 10 000.00000000.00000 002 00001 2 00003 1 00008 1 00000 0 00000 0 00000 0 0000.699600 -001.208900 0000.000000 0 10 000.00000000.00000 002 00002 1 00004 2 00009 1 00000 0 00000 0 00000 0 0001.396500 0000.001200 0000.001000 0 10 000.00000000.00000 002 00003 2 00005 1 00010 1 00000 0 00000 0 00000 0 0000.697000 0001.209900 0000.001000 0 10 000.00000000.00000 002 00004 1 00006 2 00011 1 00000 0 00000 0 00000 0 -000.699400 0001.208600 0000.000000 0 10 000.00000000.00000 002 00001 1 00005 2 00012 1 00000 0 00000 0 00000 0 -001.396500 -000.001400 -000.001000 0 10 000.00000000.00000 041 00001 1 00000 0 00000 0 00000 0 00000 0 00000 0 -001.247600 -002.165800 -000.001800 0 21 000.00000000.00000 041 00002 1 00000 0 00000 0 00000 0 00000 0 00000 0 0001.252000 -002.163700 0000.000000 0 21 000.00000000.00000 041 00003 1 00000 0 00000 0 00000 0 00000 0 00000 0 0002.499600 0000.002400 0000.001800 0 21 000.00000000.00000 041 00004 1 00000 0 00000 0 00000 0 00000 0 00000 0 0001.247700 0002.165800 0000.001800 0 21 000.00000000.00000 041 00005 1 00000 0 00000 0 00000 0 00000 0 00000 0 -001.252000 0002.163400 0000.000000 0 21 000.00000000.00000 041 00006 1 00000 0 00000 0 00000 0 00000 0 00000 0 -002.499600 -000.002600 -000.001800 0 21 000.00000000.00000 I read it in, and when I write it out to a new file, all I get is the 00012. So, that's all it is reading in or all it is writing out. How can I get my code to read the whole molecule in and then write it all back out? TIA.E-mail to subscribers: CHEMISTRY|*|ccl.net or use:E-mail to administrators: CHEMISTRY-REQUEST|*|ccl.net or usehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt-- ========================= Ahmed E. Ismail aei|*|alum.mit.edu aei|*|aya.yale.edu