From chemistry-request@server.ccl.net Tue Dec 19 02:15:40 2000 Received: from mailgw.cica.es (erika.cica.es [150.214.1.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id CAA03238 for ; Tue, 19 Dec 2000 02:15:39 -0500 Received: from simulux.us.es (IDENT:root@simulux.us.es [150.214.145.66]) by mailgw.cica.es (8.9.1/8.9.3) with ESMTP id HAA27937; Tue, 19 Dec 2000 07:10:26 +0100 (MET) Received: from localhost (rafapa@localhost) by simulux.us.es (8.9.3/8.9.3) with ESMTP id HAA22642; Tue, 19 Dec 2000 07:40:12 +0100 Date: Tue, 19 Dec 2000 07:40:11 +0100 (CET) From: Rafael Rodriguez Pappalardo To: Ali N Rashid cc: Zhenyu Lu , chemistry@ccl.net Subject: Re: CCL:IRC reaction path geometres In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Mon, 18 Dec 2000, Ali N Rashid wrote: > > > Try writing a routine that uses as input the gausian output file. Then > specify that the program write individual files with the coordinates of > each point in the reaction. Use newzmat to change the coordinates to pdb. > > There is a program called Molden that allows to make movies of IRC > calculations. This might help as well. > Before using Molden to animate an IRC calculation you shouild use the irc2xyz utility included in the Molden distribution to extract the optimized points from the Gaussian output file. Best regards, Rafael > Good luck. > > Ali > > > On Sun, 17 Dec 2000, Zhenyu Lu wrote: > > > Hi, I was using Gaussian 98, ran reaction path calculations. > > I used keyword IRC, doing forward and backword reactons. > > In the gaussian output file, you will see geometres and energes > > of each point are listed as a table. > > My question is: > > How can I convert one Gaussian output file to PDB files or XYZ > > files, each PDB/XYZ file for just one point along the reaction path? > > > > I know Gaussian provides some unitily, like newzmat, which can > > make a convertion between different file types, but I don't know how to use it > > to solve my question above. > > > > Thanks in advance. > > Zhenyu Lu > > Dept of Chem, Duke Univ. > > > > > > > > > > > -= 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 > > > > > -- Dr. Rafael R. Pappalardo Dept. Quimica Fisica, Fac. de Quimica, Univ. de Sevilla. 41012-Sevilla (Spain) e-mail: rafapa@simulux.us.es From chemistry-request@server.ccl.net Mon Dec 18 23:28:00 2000 Received: from eddings.acpub.duke.edu (eddings.acpub.duke.edu [152.3.233.76]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id XAA02672 for ; Mon, 18 Dec 2000 23:28:00 -0500 Received: from ZhenyuLu (dhcp9141.chem.duke.edu [152.3.169.141]) by eddings.acpub.duke.edu (8.9.3/8.9.3/Duke-5.0.0) with SMTP id WAA05974; Mon, 18 Dec 2000 22:22:50 -0500 (EST) Message-ID: <001d01c0696a$de6fe9a0$8da90398@chem.duke.edu> From: "Zhenyu Lu" To: Subject: parameters of amber force field for Hydroxide ion? Date: Mon, 18 Dec 2000 22:22:07 -0500 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_001A_01C06940.F5139AA0" 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 This is a multi-part message in MIME format. ------=_NextPart_000_001A_01C06940.F5139AA0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello,=20 where can I find the emperical force field paramters for the hydroxide = ion? I am modelling an enzyme system, containing Zinc ions with = water/hydroxide ligands around in the active site. For such kind of = system, is there anyone having the experience of treating it by pure = molecular mechanic method? Is the reasult of MD in agreement with the = crystal structure?=20 How about using AM1/MM or PM3/MM? =20 Thanks a lot! lu =20 =20 ------=_NextPart_000_001A_01C06940.F5139AA0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hello, 
where can I find the emperical force field paramters = for the=20 hydroxide ion?
I am modelling an enzyme = system, containing Zinc=20 ions with water/hydroxide ligands around in the active site. For such = kind of=20 system, is there anyone having the experience of treating it by pure=20  molecular mechanic method?  Is the reasult of MD in = agreement  with the crystal structure?
How about  using AM1/MM or PM3/MM?  =20
Thanks a lot!
 
lu
 
 
 
------=_NextPart_000_001A_01C06940.F5139AA0-- From chemistry-request@server.ccl.net Tue Dec 19 02:49:54 2000 Received: from web9610.mail.yahoo.com (web9610.mail.yahoo.com [216.136.129.189]) by server.ccl.net (8.8.7/8.8.7) with SMTP id CAA03477 for ; Tue, 19 Dec 2000 02:49:54 -0500 Message-ID: <20001219064442.62334.qmail@web9610.mail.yahoo.com> Received: from [161.142.4.9] by web9610.mail.yahoo.com; Mon, 18 Dec 2000 22:44:42 PST Date: Mon, 18 Dec 2000 22:44:42 -0800 (PST) From: sohail qamar Subject: HYPERCHEM'NOT GIVING H IN OUTPUT. To: chemistry@ccl.net Cc: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear friends, HAPPY EID MUBARAK-MERRY CHRISTMAS AND HAPPY NEW YEAR. When I add hydrogens in HYPERCHEM (demo version)to a pdb file .The program is not giving me Hydrogens or all atom model in the output file.It just give the output same as input. Is there any BUG in this program as mentioned in the Readme file? If there is I am not getting .bas file in CDK directory to replace it with the old one. or I am making error at the desktop menu or prefrences etc. Any suggestions... __________________________________________________ Do You Yahoo!? Yahoo! Shopping - Thousands of Stores. Millions of Products. http://shopping.yahoo.com/ From chemistry-request@server.ccl.net Tue Dec 19 13:48:21 2000 Received: from interlock.herc.com (interlock.herc.com [199.221.7.2]) by server.ccl.net (8.8.7/8.8.7) with SMTP id NAA07566 for ; Tue, 19 Dec 2000 13:48:20 -0500 From: Goutam.Das@betzdearborn.com Received: from csdnsg1.herc.com ([147.116.14.51]) by interlock.herc.com with SMTP id MAA26017 (InterLock SMTP Gateway for ); Tue, 19 Dec 2000 12:43:00 -0500 Subject: aromatic crystal_pdb/xyz To: chemistry@ccl.net X-Mailer: Lotus Notes Release 5.0.2b December 16, 1999 Message-Id: Date: Tue, 19 Dec 2000 11:41:38 -0600 X-Priority: 3 (Normal) X-Mimetrack: Serialize by Router on CSDNSG1/Servers/Herc(Release 5.0.1b|September 30, 1999) at 12/19/2000 12:31:28 PM Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear CCLers: Could anyone of you direct me to references/websites for substituted/unsubstituted polynuclear aromatic hydrocarbons--mainly naphthalenes and anthracenes? Thank you very much in anticipation and happy christmas. Goutam Das Scientist BetzDearborn Division of Hercules The Woodlands, TX 77380 281.367.6201 ext 425 From chemistry-request@server.ccl.net Tue Dec 19 13:24:20 2000 Received: from cheetah.it.wsu.edu (root@cheetah.it.wsu.edu [134.121.1.8]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA07694 for ; Tue, 19 Dec 2000 13:24:20 -0500 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 KAA32170; Tue, 19 Dec 2000 10:24:19 -0800 (PST) Message-ID: <003a01c069e8$e660b300$b4297986@chem.wsu.edu> From: "Phillip D. Matz" To: "sohail qamar" , Cc: References: <20001219064442.62334.qmail@web9610.mail.yahoo.com> Subject: Re: CCL:HYPERCHEM'NOT GIVING H IN OUTPUT. Date: Tue, 19 Dec 2000 10:24:18 -0800 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 5.00.3018.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.3018.1300 Hello Sohail Qamar! If you want hyperchem to save the hydrogens in a pdb file you have to explicitly tell it to by resaving the file with the "Save As" option under Files (or Ctrl+A). Change the "Save as type" in the "save" window to "Brookhaven PDB (*.ENT)" you will see a little area for "PDB Options" under this select "Hydrogens". Finish saving the file, when you reopen the file it should now contain the hydrogens. Let me know if this works or not for you. Hope this helps! Respectfully, Phillip Matz matz@wsunix.wsu.edu ----- Original Message ----- From: "sohail qamar" To: Cc: Sent: Monday, December 18, 2000 10:44 PM Subject: CCL:HYPERCHEM'NOT GIVING H IN OUTPUT. > Dear friends, > HAPPY EID MUBARAK-MERRY CHRISTMAS AND HAPPY NEW > YEAR. > > When I add hydrogens in HYPERCHEM (demo version)to a > pdb file .The program is not giving me Hydrogens or > all atom model in the output file.It just give the > output same as input. > Is there any BUG in this program as mentioned in the > Readme file? > If there is I am not getting .bas file in CDK > directory to replace it with the old one. > or > I am making error at the desktop menu or prefrences > etc. > Any suggestions... > > __________________________________________________ > Do You Yahoo!? > Yahoo! Shopping - Thousands of Stores. Millions of Products. > http://shopping.yahoo.com/ > > > -= 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 > > > > > From chemistry-request@server.ccl.net Tue Dec 19 16:16:09 2000 Received: from galileu.dqfex.ufpe.br (root@galileu.dqfex.ufpe.br [150.161.40.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA08363 for ; Tue, 19 Dec 2000 16:15:52 -0500 Received: from dqfex.ufpe.br (xaxado.dqf.ufpe.br [150.161.5.235]) by galileu.dqfex.ufpe.br (8.9.3/8.8.7) with ESMTP id TAA12341 for ; Tue, 19 Dec 2000 19:08:39 -0200 Message-ID: <3A3FC157.ACBB681@dqfex.ufpe.br> Date: Tue, 19 Dec 2000 18:13:12 -0200 From: Sidney Ramos X-Mailer: Mozilla 4.7 [en] (Win98; I) X-Accept-Language: en,en-US,pt-BR,ja MIME-Version: 1.0 To: CCL List Subject: Error termination via Link L609!!!! Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL Users, I have been trying to run a calculation of "Bond Order" using the keywords in the route section: # RHF/6-31G* Density=Current AIM=BO Geom=Check But the job stop and write: => Warning: RMS ERROR HAS INCREASED => Newton Step Failed for Surface Sheet 3 => Error termination via Link L609.EXE What is mean? What can I do? Thanks for any help! Best Regards, Sidney Ramos LQTC - DQF - CCEN - UFPE