From owner-chemistry@ccl.net Sat Apr 11 04:50:02 2009 From: "luisfer**edu.xunta.es" To: CCL Subject: CCL:G: Please Help me NMR INPUT FILE FOR GAUSSAIN 03 Message-Id: <-39060-090410190705-28051-Jw17QOU1RiSfNmdS5aG23w===server.ccl.net> X-Original-From: Content-Disposition: inline Content-Language: gl Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=iso-8859-1 Date: Sat, 11 Apr 2009 00:04:33 +0200 MIME-Version: 1.0 Sent to CCL by: [luisfer|,|edu.xunta.es] Dear Sarah=2E An example of input file for NMR calculatios can be as=3A =25chk=3D =2E=2E=2E =25mem=3D =2E=2E=2E mb =25nproc=3D =2E=2E=2E =23 nmr=3D( =7Bnmr-method=7D=2Cspinspin=2Cmixed) rb3lyp/6311++G(3df=2C3p= d) charge multiplicity atom 1 x1 y1 z1 atom 2 x2 y2 z2 =2E =2E =2E atom n xn yn zn = atom 1 atomic mass of 1 atom 2 atomic mass of 2 =2E =2E =2E =2E =2E =2E =2E =2E =2E atom n atomic mass of n I hope it can help you=2E Best regards=2E =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D Luis F=2E R=2E V=E1zquez Real Sociedad Espa=F1ola de Qu=EDmica Grupo de F=EDsica At=F3mica y Molecular R=FAa Tornos=2C 21=2C piso 3 15007 A Coru=F1a-GALICIA-SPAIN Tel=2E +34676300472 Correo-e luisfer=40edu=2Exunta=2Ees =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D ----- Mensaxe orixinal ----- De=3A =22Sharan sara180681=5Egmail=2Ecom=22 =3Cowner-chemistry=40ccl=2En= et=3E Data=3A Venres=2C Abril 10=2C 2009 6=3A51 am Asunto=3A CCL=3AG=3A Please Help me NMR INPUT FILE FOR GAUSSAIN 03 =3E Dear Friends =3E = =3E I am new to Gaussian i am doing my research =3E in spectroscopy investigation using Gaussian=2E I am struck in givin= g = =3E NMRinput file for Gaussian=2E =3E = =3E 1) How to specify the isotopes =3E 2) How to change the solvents for NMR =3E = =3E I don=27t know how to specify these requirements while giving NMR = =3E Input=2E Is =3E there somebody to give hand to my problem =2C it will helpful for me= =2E=2E=2E =3E = =3E Advance thanks =3E -- = =3E SARAVANAN=2EI =3E Jr=2E Scientist Chemoinformatics =3E From owner-chemistry@ccl.net Sat Apr 11 09:55:00 2009 From: "Madhavan Narayanan madi7sk_._gmail.com" To: CCL Subject: CCL: chemcraft, cubegen and density Message-Id: <-39061-090411095336-26575-ETc9kVj+VqHwexQEb/3djg%%server.ccl.net> X-Original-From: "Madhavan Narayanan" Date: Sat, 11 Apr 2009 09:53:32 -0400 Sent to CCL by: "Madhavan Narayanan" [madi7sk * gmail.com] Hi, I converted my check point file to .fchk and then to .cube. Then I tried opening it in chemcraft. When I opened it to view the electron density, I see only atoms with positive density. How do I get it to show me both positive and negative regions? I am very new to this and would appreciate any help. Thank you Madi From owner-chemistry@ccl.net Sat Apr 11 11:51:01 2009 From: "Madi madi7sk _ gmail.com" To: CCL Subject: CCL: chemcraft, cubegen and density Message-Id: <-39062-090411113837-28330-xhZUSBzW49HRM9djqi/3lg##server.ccl.net> X-Original-From: Madi Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Sat, 11 Apr 2009 11:38:20 -0400 MIME-Version: 1.0 Sent to CCL by: Madi [madi7sk-.-gmail.com] Hi All I am sorry about not wording the question properly. I meant to ask how to see regions of high and low electron densities. Right now i am able to see only one colored blob on the molecule. Thanks madi On Sat, Apr 11, 2009 at 9:53 AM, Madhavan Narayanan madi7sk_._gmail.com wrote: > > Sent to CCL by: "Madhavan =A0Narayanan" [madi7sk * gmail.com] > Hi, > > I converted my check point file to .fchk and then to .cube. > Then I tried opening it in chemcraft. When I opened it to view the electr= on density, I see only atoms with positive density. How do I get it to show= me both positive and negative regions? I am very new to this and would app= reciate any help. > > Thank you > Madi > > > > -=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 Sat Apr 11 12:35:00 2009 From: "Radoslaw Kaminski rkaminski.rk%gmail.com" To: CCL Subject: CCL:G: 6-31G** basis set in CRYSTAL06 Message-Id: <-39063-090411123138-15016-XxWg+v3RceloXUtyP6Yk3g*server.ccl.net> X-Original-From: "Radoslaw Kaminski" Date: Sat, 11 Apr 2009 12:31:34 -0400 Sent to CCL by: "Radoslaw Kaminski" [rkaminski.rk+*+gmail.com] Hello, I was trying to apply 6-31G** basis set in my periodic calculations with CRYSTAL06. My organic compound consists of C, H, O, N and S. The main problem is the sulphur atom. All basis sets found on the CRYSTAL06 website for sulphur are (I think so) optimised for some inorganic compounds thus I tried to to use this program provided in Internet (gaustocry). I have taken the Gaussian basis set format for 6-31G** (from EMSL Basis Set Exchange), converted is and used in CRYSTAL06 but then as an output I have obtained something like this: ERROR **** INPBAS **** ONLY S(0), SP(1), P(2), D(3) OR F(4) SHELL TYPES ALLOWED To be honest I am not keen on with all this basis sets modifications. I would be very appreciated if someone could help me with this problem: how to apply 6-31G** basis set for sulphur atom in CRYSTAL06. If it is impossible than I looking forward to suggestions what different basis set I could use for S in my periodic calculations. With best regards Radek From owner-chemistry@ccl.net Sat Apr 11 16:03:01 2009 From: "Stephen Bowlus chezbowlus ~ comcast.net" To: CCL Subject: CCL: transition states of enzymes Message-Id: <-39064-090411154901-28450-aUjhZwSqjs+q/vte+kBStw#server.ccl.net> X-Original-From: Stephen Bowlus Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Sat, 11 Apr 2009 12:16:02 -0700 Mime-Version: 1.0 (Apple Message framework v930.3) Sent to CCL by: Stephen Bowlus [chezbowlus/a\comcast.net] Hello, Alexandra, We used a slightly different approach to investigate the TS of chorismate mutase. The work was done in the early 90's and at workstation speeds, one needed all the shortcuts one could use. We investigated the reaction with semiempirical methods (MOPAC6) using the truncated residues inferred to be coordinated with the substrate, primarily to probe electronic effects on the TS. We did not place any restraints on the residues' geometries (the enzyme structure was not known). You can see the work in "Computer-Aided Molecular Design" ACS Symposium series 589, p 158 ff (1995). Houk and Wiest did a similar study at higher levels of theory, published in JACS in '94 (maybe '95), but I don't recall how they included the enzyme. Hope this is relevant, Steve On Apr 8, 2009, at 3:04 PM, alexandra.marques.^.fc.up.pt wrote: > > Sent to CCL by: alexandra.marques=-=fc.up.pt > Hi, > > I have been read some articles about the search for transitions > state structures in enzymatic reactions but I still have some doubts: > 1) It seems that when the full enzyme is intended to be used the > most widely used approach is to use QM/MM to model the enzyme and > perform a relaxed PES scan along some reaction coordinate. Is this > correct or there are better methods? > 2) Imagining that an approximate transition state can be identified > in a PES scan with the full enzyme, then, which method shall be used > to prove that this is the correct transition state? I am asking that > because I think a frequency calculation or even the IRC method > cannot be applied for a large system? > Can anyone help me please. > Thanks a lot > Alexandra > > > ------------------------------------------------------------------------- > A FCUP utiliza o sistema open source de webmail Horde/IMP (www.horde.org > ) > Visite: http://www.fc.up.pt/ http://info.fc.up.pt/ > > > > -= This is automatically added to each message by the mailing script > =- > To recover the email address of the author of the message, please > changehttp://www.ccl.net/chemistry/ > sub_unsub.shtml> > Job: http://www.ccl.net/jobs> >