From owner-chemistry@ccl.net Thu Jun 3 05:21:00 2010 From: "Serdar Badoglu sbadoglu/./gazi.edu.tr" To: CCL Subject: CCL: tautomer ratios Message-Id: <-42045-100603043235-1484-+Ez6V/itBiRNG+p2KmwIHg . server.ccl.net> X-Original-From: "Serdar Badoglu" Date: Thu, 3 Jun 2010 04:32:32 -0400 Sent to CCL by: "Serdar Badoglu" [sbadoglu..gazi.edu.tr] Hi CCLers, I want to obtain tautomer ratios (or per cent abundance) for a molecule by the DFT calculations. Which parameters do I need to calculate? And how should I use them to get the ratio (or abundance)? Regards. -------------------- Serdar Badoglu, MSc. From owner-chemistry@ccl.net Thu Jun 3 06:22:00 2010 From: "Gustavo A Mercier gamercier ~ yahoo.com" To: CCL Subject: CCL: Moldy 3.6 utilities. Dump file 'globbing' Message-Id: <-42046-100602203349-7665-Umg5wU1zJc42GSdLUaLaFw#server.ccl.net> X-Original-From: "Gustavo A Mercier" Date: Wed, 2 Jun 2010 19:48:00 -0400 Sent to CCL by: "Gustavo A Mercier" [gamercier/a\yahoo.com] Hi! I've done several runs using Moldy 3.6. I split these into several dump files. For a variety of reasons these are renamed as follows: mnpm_dyn_r1b_000 mnpm_dyn_r1b_001 .. mnpm_dyn_r1b_039 I get an error message when using the dumpext utility to extract the headers: dumpext -c -1 mnpm_dyn_r1b_0* It extracts the headers of the files 000 to 009 but chokes on file 010 Error message: Dump headers don't match: file"mnpm_dyn_r1b_010" However, if I apply the utility only to file mnpm_dyn_r1b_010 I can extract the header. If I use dumpext -c -1 mnpm_dyn_r1b_01*, then it chokes on mnpm_dyn_r1b_020. I can see that there is an issue with the labeling in the sequence, and it may have to do with how the utility expects the file names. Any way of giving a specific filename description that will result in the globbing of the files by the utility. Using something like mnpm_dyn_r1b_%d (as suggested by the manual) does not change the behavior. The same problem occurs when running mdvaf. Any suggestions or work arounds? Thanks! Gustavo Mercier, MD,PhD gamercier*|*yahoo.com gumercie*|*bu.edu From owner-chemistry@ccl.net Thu Jun 3 10:59:01 2010 From: "Roby Kurian Roby_Kurian.(0).umit.maine.edu" To: CCL Subject: CCL: Program to calculate chemical exchange rates from NMR spectra Message-Id: <-42047-100602134930-12801-YPl1HZ9oAKG4FqN3vCfB5w(0)server.ccl.net> X-Original-From: "Roby Kurian" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 02 Jun 2010 12:53:35 -0400 MIME-Version: 1.0 Sent to CCL by: "Roby Kurian" [Roby_Kurian/a\umit.maine.edu] Hi All, I was looking for a program to calculate chemical exchange rates from peak broadening in NMR spectra. I found an old paper (J.C.S.Dalton 1982) where they have calculated exchange rates using a program called Trigen three. I couldn't find any more info on this program or the method they used. Any suggestions much appreciated. Thanks in advance Roby Kurian Roby Kurian Graduate Student Dept of Chemistry University of Maine From owner-chemistry@ccl.net Thu Jun 3 13:38:00 2010 From: "Geoff Skillman skillman * eyesopen.com" To: CCL Subject: CCL: tautomer ratios Message-Id: <-42048-100603130318-30991-EsrbTOuQoObhzitdoXSUTg!A!server.ccl.net> X-Original-From: Geoff Skillman Content-Language: en-US Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Thu, 3 Jun 2010 09:32:50 -0700 MIME-Version: 1.0 Sent to CCL by: Geoff Skillman [skillman-,-eyesopen.com] Dear Serdar- If you are asking about aqueous-phase tautomerization, please see the curre= nt issue of the Journal of Computer-Aided Molecular Design (Volume 24, Apri= l, 2010). It contains several articles covering prospective calculation of= tautomer ratios, in particular Kast et al, Soteras et al and Ribeiro et al= . The first paper in the issue also includes an overview of computational = success at prediction of tautomer ratios in the evaluation.=20 http://www.springerlink.com/content/p56871751088 Regards, Geoff -- A. Geoffrey Skillman, MD PhD OpenEye Scientific Software, Inc. -----Original Message----- > From: owner-chemistry+skillman=3D=3Deyesopen.com(0)ccl.net [mailto:owner-chem= istry+skillman=3D=3Deyesopen.com(0)ccl.net] On Behalf Of Serdar Badoglu sbado= glu/./gazi.edu.tr Sent: Thursday, June 03, 2010 2:33 AM To: Geoff Skillman Subject: CCL: tautomer ratios Sent to CCL by: "Serdar Badoglu" [sbadoglu..gazi.edu.tr] Hi CCLers, I want to obtain tautomer ratios (or per cent abundance) for a molecule by = the DFT calculations. Which parameters do I need to calculate? And how shou= ld I use them to get the ratio (or abundance)? Regards. -------------------- Serdar Badoglu, MSc. -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Thu Jun 3 14:12:00 2010 From: "Jacqueline Cawthray jcawth01_._gmail.com" To: CCL Subject: CCL: Program to calculate chemical exchange rates from NMR spectra Message-Id: <-42049-100603131540-4324-k8H7I556PnWddTvRqKS7pQ*_*server.ccl.net> X-Original-From: Jacqueline Cawthray Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 3 Jun 2010 09:07:12 -0700 MIME-Version: 1.0 Sent to CCL by: Jacqueline Cawthray [jcawth01!A!gmail.com] Hi You can try HypNMR by Peter Gans although it's not free. http://www.hyperquad.co.uk/hypnmr.htm Good luck Jacquie Jacqueline Cawthray, Ph.D. Orvig Research Group Department of Chemistry University of British Columbia 2036 Main Mall Vancouver, BC, V6T 2A3 Email: jcawth01 ~ chem.ubc.ca On Wed, Jun 2, 2010 at 9:53 AM, Roby Kurian Roby_Kurian. ~ .umit.maine.edu wrote: > > Sent to CCL by: "Roby Kurian" [Roby_Kurian/a\umit.maine.edu] > > Hi All, > I was looking for a program to calculate chemical exchange rates from pea= k broadening in NMR spectra. I found an old paper (J.C.S.Dalton 1982) where= they have calculated exchange rates using a program called Trigen three. I= couldn't find any more > info on this program or the method they used. > > Any suggestions much appreciated. > > Thanks in advance > > Roby Kurian > > > > Roby Kurian > Graduate Student > Dept of Chemistry > University of Maine > > > > -=3D This is automatically added to each message by the mailing script = =3D-> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml> =A0 =A0 =A0http://www.ccl.net/spammers.txt> > > -- From owner-chemistry@ccl.net Thu Jun 3 22:22:00 2010 From: "Jun Zhang coolrainbow]=[yahoo.cn" To: CCL Subject: CCL: =?utf-8?B?5Zue5aSN77yaIENDTDogdGF1dG9tZXIgcmF0aW9z?= Message-Id: <-42050-100603093133-15174-9T+6zVdGjObpWNsfrNtXYg=server.ccl.net> X-Original-From: Jun Zhang Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Date: Thu, 3 Jun 2010 20:27:02 +0800 (CST) MIME-Version: 1.0 Sent to CCL by: Jun Zhang [coolrainbow .. yahoo.cn] Hi Serdar: In my opinion, you should compute the free energy difference between the ta= utomers and then use thermodynamics formalae to get the ratio Regards Jun Zhang Nankai University coolrainbow _ yahoo.cn --- 10=E5=B9=B46=E6=9C=883=E6=97=A5=EF=BC=8C=E5=91=A8=E5=9B=9B, Serdar Bado= glu sbadoglu/./gazi.edu.tr =E5=86=99=E9=81=93=EF= =BC=9A > =E5=8F=91=E4=BB=B6=E4=BA=BA: Serdar Badoglu sbadoglu/./gazi.edu.tr > =E4=B8=BB=E9=A2=98: CCL: tautomer ratios > =E6=94=B6=E4=BB=B6=E4=BA=BA: "Zhang, Jun " > =E6=97=A5=E6=9C=9F: 2010=E5=B9=B46=E6=9C=883=E6=97=A5,=E5=91=A8=E5=9B=9B,= =E4=B8=8B=E5=8D=884:32 >=20 > Sent to CCL by: "Serdar=C2=A0 Badoglu" > [sbadoglu..gazi.edu.tr] > Hi CCLers, >=20 > I want to obtain tautomer ratios (or per cent abundance) > for a molecule by the DFT calculations. Which parameters do > I need to calculate? And how should I use them to get the > ratio (or abundance)? >=20 > Regards. >=20 > -------------------- > Serdar Badoglu, MSc. >=20 >=20 >=20 > -=3D This is automatically added to each message by the > mailing script =3D- > To recover the email address of the author of the message, > please change > the strange characters on the top line to the _ sign. You > can also>=20 > E-mail to subscribers: CHEMISTRY _ ccl.net > or use: > =C2=A0 =C2=A0 =C2=A0>=20 > E-mail to administrators: CHEMISTRY-REQUEST _ ccl.net > or use > =C2=A0 =C2=A0 =C2=A0>=20 > Subscribe/Unsubscribe:=20 > =C2=A0 =C2=A0 =C2=A0>=20>=20 > Job: http://www.ccl.net/jobs=20>=20>=20> =C2=A0 =C2=A0 =C2=A0>=20>=20 >=20 > =0A=0A=0A