From chemistry-request@server.ccl.net Sun Apr 1 11:11:49 2001 Received: from netra.ksu.edu.sa ([212.138.39.67]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f31FBiD01512 for ; Sun, 1 Apr 2001 11:11:48 -0400 Received: from sun1.ksu.edu.sa (sun1.ksu.edu.sa [212.138.39.3]) by netra.ksu.edu.sa (8.9.0/8.9.0) with ESMTP id SAA15201 for ; Sun, 1 Apr 2001 18:20:45 -1700 (Mideast/Riyadh) Received: from localhost (azhary@localhost) by sun1.ksu.edu.sa (8.9.0/8.7.3) with SMTP id SAA29364 for ; Sun, 1 Apr 2001 18:08:55 -0300 (GMT) Date: Sun, 1 Apr 2001 18:08:55 -0300 (GMT) From: "Adel Abbas Ali Elazhary Sci. College" X-Sender: azhary@sun1 To: chemistry@ccl.net Subject: ECP multi jobs in Gaussin Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL members: I am calculating MP2 energy of a molecule at the HF optimized geometry. Since molecule has a K+ ion, I am using ECP for K+. After I do the HF geometry optimization and I want to calculated the MP2 energy, I use "geom=allcheck guess = read" to read the HF optimized geometry from the previous step but this does not work. I do not know why. The following is a sample input and any suggestions are greatly appreciated. Notice that this works if I do not ECP basis set. Thanking a lot in advance. Best regards, Adel El-Azhary ================================================================== #p hf/GEN 6d pseudo=cards Opt D4h (6) HF potassium 1 1 o1 0.000000 2.179675 0.000000 etc.. x, y ,z k29 0.000000 0.000000 0.000000 K 0 S 4 1.00 3.0720000 -.3084300 etc... ECP 2 17.4450910 125.5951809 2 4.4636131 23.1977649 --link1-- #p MP2(fc,fulldirect)/GEN pseudo=cards geom=allcheck guess=read D4h (6) HF/MP2 potassium 1 1 K 0 S 4 1.00 3.0720000 -.3084300 etc ... ECP 2 17.4450910 125.5951809 2 4.4636131 23.1977649 From chemistry-request@server.ccl.net Sun Apr 1 18:45:16 2001 Received: from femail13.sdc1.sfba.home.com ([24.0.95.140]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f31MjFD02365 for ; Sun, 1 Apr 2001 18:45:16 -0400 Received: from C1353359A ([65.4.172.51]) by femail13.sdc1.sfba.home.com (InterMail vM.4.01.03.20 201-229-121-120-20010223) with SMTP id <20010401224510.PALR14080.femail13.sdc1.sfba.home.com@C1353359A>; Sun, 1 Apr 2001 15:45:10 -0700 Message-ID: <002301c0bafc$61e70970$33ac0441@sttln1.wa.home.com> From: "Mark A. Thompson" To: "chinmoy ranjan" , References: <001901c0b9ef$c4a565b0$c14c1fac@CHINMOY> Subject: Re: CCL:summary of software to view metal centres of proteins Date: Sun, 1 Apr 2001 15:37:49 -0700 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2919.6600 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6600 You can try ArgusLab. It runs on Windows based PCs and is free. http://www.planaria-software.com/ ------------------------------------------------------------------------- home page: http://members.home.net/markt158/ ----- Original Message ----- From: "chinmoy ranjan" To: Sent: Saturday, March 31, 2001 7:35 AM Subject: CCL:summary of software to view metal centres of proteins > > Dear CClers, > > Few days earlier Ihad posted a message. I n responce I got the following > info . Thanks for the suggesstions. > The following is the list of suggesstions that I recieved: > > Dear CCLers, > I am trying to see the exact architecture of active site of a protein . > > Could any one tell me any software or tool (preferably free )through > which I could view the exact metal centre of the protein. I tried to > edit the PDB file and view the metal centre using rasmol but without > much success. > Thanks in advance. > From chemistry-request@server.ccl.net Sun Apr 1 20:25:16 2001 Received: from cheetah.it.wsu.edu (root@[134.121.1.8]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f320PGD02715 for ; Sun, 1 Apr 2001 20:25:16 -0400 Received: from ucis (ucis.chem.wsu.edu [134.121.41.180]) by cheetah.it.wsu.edu (8.9.3/8.9.3) with SMTP id RAA05224; Sun, 1 Apr 2001 17:25:10 -0700 (PDT) Message-ID: <002001c0bb0b$5d8ab660$b4297986@chem.wsu.edu> From: "Phillip D. Matz" To: "Adel Abbas Ali Elazhary Sci. College" , References: Subject: Re: CCL:ECP multi jobs in Gaussin Date: Sun, 1 Apr 2001 17:25:04 -0700 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Hello Adel El-Azhary, Your input file (or multi-step link), as you have described it, is set up for geom=check and not geom=allcheck. The subtle difference in the switch "check" versus "allcheck" is whether the input file (or multi-step link) should contain system's charge, multiplicity and comment line or if it should be read from the checkpoint file. Try changing your input file so it only employs "geom=check" and see if that works. Additionally, you can clean up the job by utilizing the chkbasis keyword since you are still using the same basis in the second job as was employed in the first: +++++++++++++++++++++++++++++++++++++++ --link1-- %chk=??? #p MP2(fc,fulldirect) chkbasis geom=check guess=read D4h (6) HF/MP2 potassium 1 1 +++++++++++++++++++++++++++++++++++++++ OR in a cleaner implementation +++++++++++++++++++++++++++++++++++++++ --link1-- %chk=??? #p MP2(fc,fulldirect) chkbasis geom=allcheck guess=read +++++++++++++++++++++++++++++++++++++++ Let me know if that helps! Respectfully, Phillip Matz matz@wsunix.wsu.edu ----- Original Message ----- From: "Adel Abbas Ali Elazhary Sci. College" To: Sent: Sunday, April 01, 2001 2:08 PM Subject: CCL:ECP multi jobs in Gaussin > Dear CCL members: > > I am calculating MP2 energy of a molecule at the HF optimized geometry. Since > molecule has a K+ ion, I am using ECP for K+. After I do the HF geometry > optimization and I want to calculated the MP2 energy, I use "geom=allcheck > guess = read" to read the HF optimized geometry from the previous step but > this does not work. I do not know why. The following is a sample input and > any suggestions are greatly appreciated. Notice that this works if I do not > ECP basis set. > > Thanking a lot in advance. > > Best regards, > > Adel El-Azhary > > ================================================================== > > #p hf/GEN 6d pseudo=cards Opt > > D4h (6) HF potassium > > 1 1 > o1 0.000000 2.179675 0.000000 > > etc.. x, y ,z > > k29 0.000000 0.000000 0.000000 > > K 0 > S 4 1.00 > 3.0720000 -.3084300 > > etc... ECP > > 2 17.4450910 125.5951809 > 2 4.4636131 23.1977649 > > --link1-- > > #p MP2(fc,fulldirect)/GEN pseudo=cards geom=allcheck guess=read > > D4h (6) HF/MP2 potassium > > 1 1 > > K 0 > S 4 1.00 > 3.0720000 -.3084300 > > etc ... ECP > > 2 17.4450910 125.5951809 > 2 4.4636131 23.1977649 > > > > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > >