From owner-chemistry@ccl.net Tue Jul 19 08:52:39 2005 From: "CCL" To: CCL Subject: CCL: energy of the first excited state Message-Id: <-28904-050719084937-11245-eSc6C2yCCSce8pLLLmWjCA]=[server.ccl.net> X-Original-From: "ÑîÕñÄÈ" Content-Type: text/plain Sent to CCL by: "ÑîÕñÄÈ" I have another problem to trouble you. Please help me. This is the input file #P cis(direct)/6-31+G** density=current opt=z-matrix gfinput iop(6/7=3) test > from the output file I get the following informations first, Excitation energies and oscillator strengths: Excited State 1: Singlet-A' 3.8548 eV 321.63 nm f=0.5311 62 -> 63 0.52533 62 -> 65 -0.41883 This state for optimization and/or second-order correction. Total Energy, E(CIS) = -794.462358789 The other two excited states is useless for my question, so I don¡¯t copy it. My question is whether E(CIS) = -794.462358789 is the energy of the first excited state in cis/6-31£«G** level. Second, in the last of the output file, I get HF=-794.604021. what is the meaning of it, whether this one is the energy of the first excited state. What is the meaning of HF. In conclusion, E(CIS) = -794.462358789 and HF=-794.604021, which one is the energy of the first excited state in cis/6-31£«G** level. From owner-chemistry@ccl.net Tue Jul 19 10:52:36 2005 From: "CCL" To: CCL Subject: CCL: Re: Drawing in Linux Message-Id: <-28905-050719103515-1427-eSc6C2yCCSce8pLLLmWjCA^_^server.ccl.net> X-Original-From: =?ISO-8859-1?Q?David_Hugas_Germ=E0?= Content-Type: multipart/mixed; boundary="------------030605030406080801090001" MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?David_Hugas_Germ=E0?= This is a multi-part message in MIME format. --------------030605030406080801090001 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit Hi, The ChemDraw "clone" for linux that I've been using is XDrawChem. You can find it at http://xdrawchem.sourceforge.net . It's quite compatible with ChemDraw format, although there are files that I can't open or crash. The reason could be that the last version of XDrawChem doesn't have all the characteristics ChemDraw has. Anyway, there ara other packages like ChemTool, but I haven't tried them. Cheers! David. En/na CCL ha escrit: > Hello! I was wondering if anyone would know a program like ChemDraw > for Linux? > Thank you all in advance, > Fleming -- --------------------------------------- David Hugas i Germà Institut de Química Computacional Facultat de Ciències (Campus Montilivi) Universitat de Girona 17071, Girona, Catalonia (Spain) Tlf:972.418358 e-mail:davidh^_^iqc.udg.es --------------------------------------- --------------030605030406080801090001 Content-Type: text/x-vcard; charset=utf-8; name="davidh.vcf" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="davidh.vcf" begin:vcard fn;quoted-printable:David Hugas Germ=C3=A0 n;quoted-printable:Hugas Germ=C3=A0;David org;quoted-printable:Universitat de Girona;Institut de Qu=C3=ADmica Computacional adr;quoted-printable:Campus Montilivi S/N;;Facultat de Ci=C3=A8ncies;Girona;Girona;17071;Catalunya email;internet:davidh^_^iqc.udg.es title:Sr. tel;work:+34.972.418358 tel;fax:+34.972.418356 tel;cell:+34.679.359413 x-mozilla-html:FALSE url:http://iqc.udg.es/~davidh version:2.1 end:vcard --------------030605030406080801090001-- From owner-chemistry@ccl.net Tue Jul 19 15:39:48 2005 From: "CCL" To: CCL Subject: CCL: W:Applications of Web-based Services in Drug Discovery Message-Id: <-28907-050719153900-8015-eSc6C2yCCSce8pLLLmWjCA-,-server.ccl.net> X-Original-From: "Barry Hardy" Sent to CCL by: "Barry Hardy" In our eCheminfo Community of Practice meetings this Autumn we are bringing together top researchers from industry, academia and research institutes including Merck, Johnson & Johnson, NCBI, NIH, EBI, SIB etc. in meetings in Philadelphia, US and Basel, Switzerland to present and discuss latest developments in Web services of relevance to drug discovery. Aligned with knowledge management principles a significant amount of meeting time will be reserved for question and discussion time for all participants in these meetings. Additional views, poster presentations, semantic web and web services demonstrations are particularly welcome. We hope that these discussions will lead to new initiatives and indeed further ongoing discussion and conversations in this key area of knowledge transfer and flow to enable improved knowledge integration, productivity and innovation in life science and drug discovery. I hope you can join us in Philadelphia or Basel, or if that is not possible, please signup and join us virtually through the eCheminfo web site. Please also feel free to email or call me here to discuss any interests or proposals you have for this program activity. best regards Barry Hardy eCheminfo Community of Practice Manager http://echeminfo.com/ Douglas Connect, Switzerland +41 61 851 0170 (office) Applications of Web-based Services in Drug Discovery...more information on: Pharmaceutical research is under challenge to improve the choice, quality and safety of lead candidates. There is a clear need for an open discussion and an awareness of the requirements for a much more complex knowledge management and knowledge transfer between academic, government and commercial interests. The semantic web has the potential to make significant contributions to the drug discovery of the future but is at this time at an early development stage and there are only a few public tools for the data mining and sharing of chemical information. Just a few years ago, the only imaginable way of doing in silico drug design - or, indeed, any cheminformatics research - was to use in-house and commercial software and databases. New developments in Web services however are offering todays researchers additional resources. Although cheminformatics admittedly lags far behind bioinformatics (where an enormous wealth of data and software is literally a click away), we are beginning to see some chemical resources in open access. A goal for this program on "Web-based Services in Drug Design" is to present some of the possibilities of web-based tools and data and to lead into discussions on how can web services work for both the academic world and industry, while maintaining commercial, ip and security concerns? What potential impact could they have on discovery productivity? What are the best sustainable business models that can be applied to such services? How significant are the benefits of increased upstream and downstream knowledge flow due to services based on ontology frameworks? What are the key current hindrances to be overcome for the integration of web services into drug discovery in the chemical information area? The following meeting sessions are planned: eCheminfo InterAction Meeting Session, Philadelphia, 11 October 2005 Applications of Web-based Services in Drug Discovery chaired by Marc Nicklaus, (National Institutes of Health) Presenters & Discussion Leaders: A Web-based Chemoinformatics System for Drug Discovery, Brett Tounge (Johnson & Johnson) Web enabling technology for the design, enumeration, optimization and tracking of compound libraries, Brad Feuston (Merck) ZINC web services - providing 3D structures of purchasable compounds for virtual screening to humans and machines, John Irwin (UCSF) Pubchem, Steve Bryant (NCBI) Search-and-query Information System for the Study and Discovery of Novel Agents in the Treatment of Cancer, David Covell (NCI) eCheminfo InterAction Meeting Session, Basel, Switzerland, 10 November 2005 Applications of Web-based Services in Drug Discovery chaired by Kim Henrick (European Bioinformatics Institute) Presenters & Discussion Leaders: Investigating chemical trends in the context of ligand-protein complexes by using on-line data analysis directly on the web, Dimitris Dimitropoulos (European Bioinformatics Institute) The Representation of Chemical Structures and its Application to Property Prediction, Johann Gasteiger (Universitaet Erlangen-Nuernberg) Open Archives as a Route for the Capture, Dissemination and Access to Chemical Information, Simon Coles (University of Southampton) Identification of biological units in protein crystals, Eugene Krissinel (European Bioinformatics Institute) SWISS-MODEL Server and Repository: Web based resources for comparative protein structure modeling and their application in drug discovery, Torsten Schwede (University of Basel) Posters All registrants for the eCheminfo InterAction meetings and the above Web Services sessions are eligible to submit a Conference Poster. Attendees may view and discuss the Posters and leave messages for the authors on the Web site. Electronic poster session and software demonstrations will additionally be scheduled to take place on a wireless network at the US and European InterAction Meetings. Poster Abstracts (of ca. 300 words) with Title, Institution, Authors and Contact Information should be submitted for consideration to echeminfo at douglasconnect.com Conference Posters can be presented as HTML, pdf, Powerpoint or Word documents and can include live demonstrations on the Web. Barry Hardy, PhD barry.hardy at tiscalinet.ch Douglas Connect, Switzerland +41 61 851 0170 (office) From owner-chemistry@ccl.net Tue Jul 19 15:31:57 2005 From: "CCL" To: CCL Subject: CCL: Help to use NWCHEM Message-Id: <-28906-050719143510-916-eSc6C2yCCSce8pLLLmWjCA-,-server.ccl.net> X-Original-From: Delwar Hossain Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1242617612-1121794506=:95703" MIME-Version: 1.0 Sent to CCL by: Delwar Hossain --0-1242617612-1121794506=:95703 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear CCL member, I am trying to use NWCHEM for DFT calculation. When I run job, I got error message which I am unable to detect and solve. I will be grateful to you if you kindly help me to solve the problem. With best regards, Sincerely yours Delwar Hossain hossaind2004-,-yahoo.com The detail iformation is as follows: PBS Script: #PBS -N nwc_02 #PBS -l nodes=2:ppn=2 #PBS -l walltime=48:00:00 #PBS -V #PBS -S /bin/bash #PBS -r n cd $PBS_O_WORKDIR export JOBDIR='/home/delwar/nwc_gepossT10li' export RESDIR='/home/delwar/nwc_gepossT10li' export INIDIR='/home/delwar/nwc_gepossT10lii' export SRCDIR='/usr/local/NWChem/bin' echo $JOBDIR cd $JOBDIR cat $PBS_NODEFILE | sort | uniq > mfile /usr/bin/mpirun -np 4 -mach_file $PBS_NODEFILE $SRCDIR/nwchem get10li.nw* >& output Input fule: START "get10li" title "get10li cage +1 state" memory total 900 mb permanent_dir . scratch_dir . charge 1 GEOMETRY autosym Ge -2.463788 -1.644679 -1.672689 Ge 1.026352 2.777996 1.672983 ---------------------------------------------- ---------------------------------------------- O -2.372170 0.094069 -1.883851 O -0.822363 -2.226157 -1.882592 O 1.207494 3.268003 0.000000 O -2.736178 2.158110 0.000000 --------------------------------------------- --------------------------------------------- H -3.246605 2.562704 2.634155 H -3.437726 -2.297464 2.634044 H 1.432246 3.878159 -2.633919 H -3.246604 2.562704 -2.634155 Li -0.00092 -0.000003 0.000000 END BASIS H library 6-311G* O library 6-311G* Ge library "LANL2DZ ECP" Li library 6-311G* END DFT direct iterations 50 XC vwn_1_rpa 0.19 lyp 0.81 HFexch 0.20 slater 0.80 becke88 nonlocal 0.72 END task dft energy numerical Output error message: Tag Description Shells Functions and Types ---------------- ------------------------------ ------ --------------------- H 6-311G* 3 3 3s O 6-311G* 8 19 4s3p1d Ge LANL2DZ ECP 4 8 2s2p Li 6-311G* 8 19 4s3p1d hdbm_fseek: Stale NFS file handle write_file_entry: failed to position file rtdb_seq_put_info: put failed for "basis:ao basis:bs_nr_tags" in ./get10li.db bas_rtdb_store: ERROR one or more put operations failed ------------------------------------------------------------------------ bas_input: failed to store basis 0 ------------------------------------------------------------------------ ------------------------------------------------------------------------ current input line : 51: END ------------------------------------------------------------------------ ------------------------------------------------------------------------ There is an error in the specified basis set ------------------------------------------------------------------------ For more information see the NWChem manual at http://www.emsl.pnl.gov/docs/nwchem/nwchem.html For further details see manual section: 0:0:bas_input: failed to store basis:: 0 0:0:bas_input: failed to store basis:: 0 Last System Error Message from Task 0:: Invalid argument 0: ARMCI aborting 0 (0). 0: ARMCI aborting 0 (0). system error message: Invalid argument ----------------------------------------------------------------------------------------------------------------------- geom_rtdb_load: not found or rtdb corrupt: geometry -> geometry geom_rtdb_load: open geometies: 1 1 geom_rtdb_load: "geometry" -> "geometry" geom_rtdb_load: geometries in last accessed data base: 1 geometry ------------------------------------------------------------------------ rdinput: no geometry 72 ------------------------------------------------------------------------ ------------------------------------------------------------------------ current input line : 58: task dft energy numerical ------------------------------------------------------------------------ ------------------------------------------------------------------------ An error occured in the Runtime Database ------------------------------------------------------------------------ For more information see the NWChem manual at http://www.emsl.pnl.gov/docs/nwchem/nwchem.html For further details see manual section: & nbsp; 0:0:rdinput: no geometry:: 72 Last System Error Message from Task 0:: Permission denied 0: ARMCI aborting 72 (0x48). system error message: Permission denied 0:0:rdinput: no geometry:: 72 0: ARMCI aborting 72 (0x48). ------------------------------------------------------------------------------------------------------------------------------- current input line : 58: task dft energy numerical ------------------------------------------------------------------------ ------------------------------------------------------------------------ This error has not yet been assigned to a category ------------------------------------------------------------------------ For more information see the NWChem manual at http://www.emsl.pnl.gov/docs/nwchem/nwchem.html For further details see manual section: No section for this category ; 0:0:atomscf:atomd: error in atom scf:: 0 0:0:atomscf:atomd: error in atom scf:: 0 0: ARMCI aborting 0 (0). Last System Error Message from Task 0:: Permission denied 0: ARMCI aborting 0 (0). system error message: Permission denied 0:0:atomscf:atomd: error in atom scf:: 0 __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com --0-1242617612-1121794506=:95703 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Dear CCL member,
I am trying to use NWCHEM for DFT calculation. When I run job, I got error message which I am unable to detect and solve.
I will be grateful to you if you kindly help me to solve the problem.
With best regards,
Sincerely yours
Delwar Hossain
 
The detail iformation is as follows:
 
PBS Script:
 
#PBS -N nwc_02
#PBS -l nodes=2:ppn=2
#PBS -l walltime=48:00:00
#PBS -V
#PBS -S /bin/bash
#PBS -r n
cd $PBS_O_WORKDIR
export JOBDIR='/home/delwar/nwc_gepossT10li'
export RESDIR='/home/delwar/nwc_gepossT10li'
export INIDIR='/home/delwar/nwc_gepossT10lii'
export SRCDIR='/usr/local/NWChem/bin'
echo $JOBDIR
cd $JOBDIR
cat $PBS_NODEFILE | sort | uniq > mfile
/usr/bin/mpirun -np 4 -mach_file $PBS_NODEFILE $SRCDIR/nwchem get10li.nw* >& output
Input fule:
 
START "get10li"
title "get10li cage +1 state"
memory total 900 mb
permanent_dir .
scratch_dir .
charge 1
GEOMETRY autosym
Ge -2.463788 -1.644679 -1.672689
Ge 1.026352 2.777996 1.672983
----------------------------------------------
----------------------------------------------
O -2.372170 0.094069 -1.883851
O -0.822363 -2.226157 -1.882592
O 1.207494 3.268003 0.000000
O -2.736178 2.158110 0.000000
---------------------------------------------
---------------------------------------------
H -3.246605 2.562704 2.634155
H -3.437726 -2.297464 2.634044
H 1.432246 3.878159 -2.633919
H -3.246604 2.562704 -2.634155
Li -0.00092 -0.000003 0.000000
END
BASIS
  H  library 6-311G*
  O  library 6-311G*
  Ge library "LANL2DZ ECP"
  Li library 6-311G*
END
DFT
  direct
  iterations 50
  XC vwn_1_rpa 0.19 lyp 0.81 HFexch 0.20  slater 0.80 becke88 nonlocal 0.72
END
task dft energy numerical
 
 
Output error message:
 
       Tag                 Description            Shells   Functions and Types
 ---------------- ------------------------------  ------  ---------------------
 H                          6-311G*                  3        3   3s
 O                          6-311G*                  8       19   4s3p1d
 Ge                       LANL2DZ ECP                4        8   2s2p
 Li                         6-311G*                  8       19   4s3p1d

hdbm_fseek: Stale NFS file handle
write_file_entry: failed to position file
rtdb_seq_put_info: put failed for "basis:ao basis:bs_nr_tags" in ./get10li.db
  bas_rtdb_store: ERROR
  one or more put operations failed
 ------------------------------------------------------------------------
 bas_input: failed to store basis        0
 ------------------------------------------------------------------------
 ------------------------------------------------------------------------
  current input line :
    51: END
 ------------------------------------------------------------------------
 ------------------------------------------------------------------------
 There is an error in the specified basis set
 ------------------------------------------------------------------------
 For more information see the NWChem manual at
 http://www.emsl.pnl.gov/docs/nwchem/nwchem.html

 For further details see manual section:
 
0:0:bas_input: failed to store basis:: 0
0:0:bas_input: failed to store basis:: 0
Last System Error Message from Task 0:: Invalid argument
  0: ARMCI aborting 0 (0).
  0: ARMCI aborting 0 (0).
system error message: Invalid argument
 
 
-----------------------------------------------------------------------------------------------------------------------
 geom_rtdb_load: not found or rtdb corrupt: geometry -> geometry
 geom_rtdb_load: open geometies:  1
  1 geom_rtdb_load: "geometry" -> "geometry"
 geom_rtdb_load: geometries in last accessed data base:  1
 geometry
 ------------------------------------------------------------------------
 rdinput: no geometry        72
 ------------------------------------------------------------------------
 ------------------------------------------------------------------------
  current input line :
    58: task dft energy numerical
 ------------------------------------------------------------------------
 ------------------------------------------------------------------------
 An error occured in the Runtime Database
 ------------------------------------------------------------------------
 For more information see the NWChem manual at           
 http://www.emsl.pnl.gov/docs/nwchem/nwchem.html        

 For further details see manual section:
                                                                                                                                                                    & nbsp;                                                       
0:0:rdinput: no geometry:: 72
Last System Error Message from Task 0:: Permission denied
  0: ARMCI aborting 72 (0x48).
system error message: Permission denied
0:0:rdinput: no geometry:: 72
  0: ARMCI aborting 72 (0x48).
-------------------------------------------------------------------------------------------------------------------------------
 current input line :
    58: task dft energy numerical
 ------------------------------------------------------------------------
 ------------------------------------------------------------------------
 This error has not yet been assigned to a category
 ------------------------------------------------------------------------
 For more information see the NWChem manual at
 http://www.emsl.pnl.gov/docs/nwchem/nwchem.html

 For further details see manual section: No section for this category                                                                                                                                                                      ;                          
0:0:atomscf:atomd: error in atom scf:: 0
0:0:atomscf:atomd: error in atom scf:: 0
  0: ARMCI aborting 0 (0).
Last System Error Message from Task 0:: Permission denied
  0: ARMCI aborting 0 (0).
system error message: Permission denied
0:0:atomscf:atomd: error in atom scf:: 0
 

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http://mail.yahoo.com --0-1242617612-1121794506=:95703-- From owner-chemistry@ccl.net Tue Jul 19 21:41:24 2005 From: "CCL" To: CCL Subject: CCL: Morse potential parameters Message-Id: <-28908-050718224736-8130-eSc6C2yCCSce8pLLLmWjCA^_^server.ccl.net> X-Original-From: skpang^_^ctimail.com Sent to CCL by: skpang^_^ctimail.com Dear all, Can the output data from the Frequency command of Gaussian 03 be used for determination of the Morse potential parameters, such as the depth of potential energy minimum (De) and force constant (k) for one particular vibrational mode? Thank you for your attention. Regards, Patrick Pang My e-mail address: skpang^_^ctimail.com