From owner-chemistry@ccl.net Mon Feb 12 08:29:00 2007 From: "ilhan yavuz ilhanyav|*|gmail.com" To: CCL Subject: CCL: anharmonic correction (format problem) Message-Id: <-33585-070212070304-16882-htjth6KDOE13Obn5B+J3vg^server.ccl.net> X-Original-From: "ilhan yavuz" Date: Mon, 12 Feb 2007 07:03:00 -0500 Sent to CCL by: "ilhan yavuz" [ilhanyav/./gmail.com] hi, I have been studying on formic acid clusters and recently I am trying to compute anharmonic corrections for C2h formic acid. I wanted to submit a job using GAMESS-US under unix enviroment. But there is an input problem which I could not recover and I want a helping hand form you. Here is the message and the input file: This is the failure message: HESS GROUP READ FROM CARDS ENERGY IS -377.5489638489 E(NUC) IS 234.5673798262 ****** FORTRAN RUN-TIME SYSTEM ****** Error 1080: unexpected character in integer field Location: the READ statement at line 640 of "hess.f" Unit: 5 and this is the input file: CONTRL RUNTYP=VSCF COORD=CART END SYSTEM TIMLIM=40000 MWORDS=150 MEMDDI=150 PARALL=.TRUE. END DIPDR READ=.TRUE. END HESS RDHESS=.T. END VIBSCF READV=.TRUE. END BASIS GBASIS=N31 NGAUSS=6 NDFUNC=1 END DATA FADsym.....rhf/6-31G(d) Cn 1 C 6.0 -1.9412958260 0.2471497224 0.0000654261 C 6.0 1.9413415844 -0.2454247308 0.0008878817 H 1.0 -3.0143681173 0.3902642900 -0.0008296593 H 1.0 3.0136952513 -0.3944759755 0.0022212827 ....etc. END HESS ENERGY IS -377.5489638489 E(NUC) IS 234.5673798262 1 1 1.06089604E+00 1.96735497E-01-3.28534312E-04-6.42306799E-03 2.34748888E-03 1 2-7.71347567E-07-3.49363136E-01 3.39102645E-02-1.58028135E-04 5.03686547E-04 1 3-1.50414630E-04 1.96920162E-06 1.92257411E-03-3.95138754E-03- 1.15070866E-05 1 4 3.33478212E-03-3.42577713E-04-1.28724088E-06-2.11185054E-01 8.54563333E-02 .......etc. END DIPDR 6.67252066E+00 4.03923503E-01 2.10342207E-03 8.99290910E-01 1.00311351E+01-1.51422171E-03 3.43342891E-05-2.57999363E-03 2.56299466E+00 6.66901556E+00 3.98193416E-01 3.34140092E-03 ....etc. END thanks for now ilhan From owner-chemistry@ccl.net Mon Feb 12 09:04:00 2007 From: "kalyan chaitanya pulipaka kalyanpulipaka/./gmail.com" To: CCL Subject: CCL: Query regarding Autodock Message-Id: <-33586-070211235649-11563-/9f9YzD8tXQeff99glxWtw-$-server.ccl.net> X-Original-From: "kalyan chaitanya pulipaka" Date: Sun, 11 Feb 2007 23:56:45 -0500 Sent to CCL by: "kalyan chaitanya pulipaka" [kalyanpulipaka- -gmail.com] Hi all, Iam working on docking using Autodock, iam stuck with a unknown problem "iam following the user guide of Autodock and trying to dock the receptor and ligand, iam able to prepare the pdb file, macromolecule, ligand also able generate grid and GPF but when iam trying to execute the AUTOGRID command it is not producing the output file" can any one please help me in this regard, Regards, P.Kalyan Chaitanya, Research scholar, Dept. of Chemistry, Nizam college, Osmania University, Hyderabad, India. From owner-chemistry@ccl.net Mon Feb 12 09:39:00 2007 From: "kalyan chaitanya pulipaka kalyanpulipaka-#-gmail.com" To: CCL Subject: CCL: Query regarding Autodock Message-Id: <-33587-070212062624-13595-ar9tBHsI5oWy8YJEwBLwzw]=[server.ccl.net> X-Original-From: "kalyan chaitanya pulipaka" Date: Mon, 12 Feb 2007 06:26:20 -0500 Sent to CCL by: "kalyan chaitanya pulipaka" [kalyanpulipaka(-)gmail.com] Hi All, iam working on Docking using Autodock and iam stuck with some unknown(for me) problem, can any one please respond who have been using or worked with Autodock before. Desciption of my problem: After preparation of Macromolecule and Ligand, setting Grid parameter file, when iam trying to run Autogrid3, it is not generating any output file. Thank you, P.Kalyan Chaitanya, Rsearch Scholar, Dept. Of Chemistry, Nizam College, Osmania University, Hyderabad-500045 India. From owner-chemistry@ccl.net Mon Feb 12 10:49:00 2007 From: "Xie Wang xie.wang===gmail.com" To: CCL Subject: CCL:G: question about GAUSSIAN casscf in pcm Message-Id: <-33589-070212093123-26644-3BJK3toJGOsUzCaMkOZIEQ**server.ccl.net> X-Original-From: "Xie Wang" Date: Mon, 12 Feb 2007 09:31:19 -0500 Sent to CCL by: "Xie Wang" [xie.wang]![gmail.com] Dear all, I have some questions about using casscf in scrf with G03. Any help will be appreciated! 1. When doing stateaverage casscf in solution using PCM model, is the solvation equilibrated with the ground state or the nroot=n excited state or some average of states? 2. When using MP2 keyword with stateaverage casscf, the MP2 energy is only calculated for the nroot=n excited state. Is there anyway that I can get the CASMP2 energy for ground state and other lower excited states from this stateaverage casscf too? 3. In the g03 manual, page 206, it is indicated that casscf pcm calculations of non equilibrium solvation can be performed using the NonEq=type PCM keyword. But this keyword is not described elsewhere in the manual. I searched around (web, on-line manual) but found no place documenting this keyword. Is it missed from the manual? Does anyone know how to use this keyword? Thanks a lot in advance! Xie From owner-chemistry@ccl.net Mon Feb 12 12:02:01 2007 From: "Antje Wolf antje.wolf*|*scai.fraunhofer.de" To: CCL Subject: CCL: Query regarding Autodock Message-Id: <-33590-070212113029-26506-iBRY3W2hc6JBZ63TF7hA8Q.@.server.ccl.net> X-Original-From: Antje Wolf Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 12 Feb 2007 16:43:53 +0100 MIME-Version: 1.0 Sent to CCL by: Antje Wolf [antje.wolf*scai.fraunhofer.de] Dear Kalyan, there is a special AutoDock mailing list. The archive is searchable at http://mgldev.scripps.edu/pipermail/autodock/. There have been similar questions before. If you don't find an answer there, write an e-mail to the list autodock-x-scripps.edu. Regards, Antje kalyan chaitanya pulipaka kalyanpulipaka-#-gmail.com wrote: >Sent to CCL by: "kalyan chaitanya pulipaka" [kalyanpulipaka(-)gmail.com] >Hi All, > >iam working on Docking using Autodock and iam stuck with some unknown(for me) problem, can any one please respond who have been using or worked with Autodock before. > >Desciption of my problem: > >After preparation of Macromolecule and Ligand, setting Grid parameter file, when iam trying to run Autogrid3, it is not generating any output file. > >Thank you, > >P.Kalyan Chaitanya, >Rsearch Scholar, >Dept. Of Chemistry, >Nizam College, >Osmania University, Hyderabad-500045 >India.> > > > > > -- Antje Wolf Fraunhofer-Institute for Algorithms and Scientific Computing (SCAI) Department of Bioinformatics Schloss Birlinghoven 53754 Sankt Augustin Germany Tel.: +49 2241 14 2537 E-mail: Antje.Wolf-x-scai.fraunhofer.de Internet: http://www.scai.fraunhofer.de From owner-chemistry@ccl.net Mon Feb 12 16:32:01 2007 From: "Shobe, David David.Shobe..sud-chemie.com" To: CCL Subject: CCL: GAMESS -- unblocking Distributed Data Interface Message-Id: <-33591-070212094711-6888-PnHudjvLtEoO+fIN01M+Cw^_^server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C74EB2.0B3A557A" Date: Mon, 12 Feb 2007 15:28:19 +0100 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [David.Shobe=-=sud-chemie.com] This is a multi-part message in MIME format. ------_=_NextPart_001_01C74EB2.0B3A557A Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable I am using the GAMESS-US compiled 2/22/06 with CygWin gcc 3.4.4. =20 When I first ran GAMESS (one of the test files) , there was a message box asking if I wanted to allow external access to my computer. The choices were "permit" or "block". I couldn't think of a reason why GAMESS would need this, so I chose "block." =20 Soon I found out that I made the wrong choice. The GAMESS output file contains only the following. And I am not offered the permit/block choice again ! What can I do?=20=20 =20 --David Shobe =20 +++++++++++ Contents of the output file: =20 Distributed Data Interface kickoff program. Initiating 1 compute processes on 1 nodes to run the following command: C:\WinGAMESS/gamess.06.exe exam01=20 TCP connect error: ETIMEDOUT. TCP: Connect failed. carbon -> carbon:3004. A fatal error occurred on DDI Process 1. TCP connect error: ETIMEDOUT. TCP: Connect failed. carbon -> carbon:3004. A fatal error occurred on DDI Process 0. ddikick.x: Sending kill signal to DDI processes. ddikick.x: Execution terminated due to error(s). ----- accounting info ----- =20 ________________________________ Don't pick lemons. See all the new 2007 cars at Yahoo! Autos. =20 This e-mail message may contain confidential and / or privileged informatio= n. If you are not an addressee or otherwise authorized to receive this mess= age, you should not use, copy, disclose or take any action based on this e-= mail or any information contained in the message. If you have received this= material in error, please advise the sender immediately by reply e-mail an= d delete this message.=20 Thank you. ------_=_NextPart_001_01C74EB2.0B3A557A Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable
I am using the GAMESS-US compiled 2/22/06 with CygWin gcc 3.4.4.
 
When I first ran GAMESS  (one of= the=20 test files) , there was a message box asking if I wanted to all= ow=20 external access to my computer.   The choices were "permit" or=20 "block".  I couldn't think of a reason why GAMESS would need this, so = I=20 chose "block."
 
Soon I found out that I made the wrong choice.  The GAMESS output= file=20 contains only the following.  And I am not offered the permit/block ch= oice=20 again !  What can I=20 do?  
 
--David Shobe
 
+++++++++++
Contents of the output file:
 
Distributed Data Interface kickoff program.
Initiating 1 compute processes on 1 nodes to run the following=20 command:
C:\WinGAMESS/gamess.06.exe exam01
TCP connect error: ETIMEDOUT.
TCP: Connect failed. carbon -> carbon:3004.
A fatal error occurred on DDI Process 1.
TCP connect error: ETIMEDOUT.
TCP: Connect failed. carbon -> carbon:3004.
A fatal error occurred on DDI Process 0.
ddikick.x: Sending kill signal to DDI processes.
ddikick.x: Execution terminated due to error(s).
----- accounting info -----
 

Don't pick lemons.
See all the new=20 2007 cars at Yahoo!=20 Autos.
This e-mail message may contain confidential and / or privileged informatio= n. If you are not an addressee or otherwise authorized to receive this mess= age, you should not use, copy, disclose or take any action based on this e-= mail or any information contained in the message. If you have received this= material in error, please advise the sender immediately by reply e-mail an= d delete this message.
Thank you.
------_=_NextPart_001_01C74EB2.0B3A557A-- From owner-chemistry@ccl.net Mon Feb 12 21:07:00 2007 From: "Brian Salter-Duke b_duke _ bigpond.net.au" To: CCL Subject: CCL: GAMESS -- unblocking Distributed Data Interface Message-Id: <-33592-070212192926-16500-oqEwjiEV4zsx98DZWEnpBg#server.ccl.net> X-Original-From: Brian Salter-Duke Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Tue, 13 Feb 2007 10:28:07 +1100 Mime-Version: 1.0 Sent to CCL by: Brian Salter-Duke [b_duke(0)bigpond.net.au] On Mon, Feb 12, 2007 at 03:28:19PM +0100, Shobe, David David.Shobe..sud-chemie.com wrote: > I am using the GAMESS-US compiled 2/22/06 with CygWin gcc 3.4.4. > > When I first ran GAMESS (one of the test files) , there was a message > box asking if I wanted to allow external access to my computer. The > choices were "permit" or "block". I couldn't think of a reason why > GAMESS would need this, so I chose "block." > > Soon I found out that I made the wrong choice. The GAMESS output file > contains only the following. And I am not offered the permit/block > choice again ! What can I do? Just relink. The new executable will ask you again. There is probably a better way, but that should fix it. > --David Shobe > > +++++++++++ > Contents of the output file: > > Distributed Data Interface kickoff program. > Initiating 1 compute processes on 1 nodes to run the following command: > C:\WinGAMESS/gamess.06.exe exam01 > TCP connect error: ETIMEDOUT. > TCP: Connect failed. carbon -> carbon:3004. > A fatal error occurred on DDI Process 1. > TCP connect error: ETIMEDOUT. > TCP: Connect failed. carbon -> carbon:3004. > A fatal error occurred on DDI Process 0. > ddikick.x: Sending kill signal to DDI processes. > ddikick.x: Execution terminated due to error(s). > ----- accounting info ----- > > > ________________________________ > > Don't pick lemons. > See all the new 2007 cars > Dc2BHNlYwNtYWlsdGFncwRzbGsDbmV3Y2Fycw--> at Yahoo! Autos. > Dc2BHNlYwNtYWlsdGFncwRzbGsDbmV3Y2Fycw--> > > This e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. > Thank you. -- Brian Salter-Duke (Brian Duke) b_duke:_:bigbond.net.au Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia Phone 03-93992847. http://www.salter-duke.bigpondhosting.com/brian/index.htm Honorary Researcher Fellow, Dept. of Medicinal Chemistry, Monash Univ.