From owner-chemistry@ccl.net Fri May 13 07:54:00 2011 From: "mirage . m.o.m : live.fr" To: CCL Subject: CCL: installation of gar2ed Message-Id: <-44630-110513075119-1208-2hOr27a7oHdOIwV9IU7jjQ#,#server.ccl.net> X-Original-From: "mirage ." Content-Type: multipart/alternative; boundary="_6c77085a-012b-4f42-8828-93894487d627_" Date: Fri, 13 May 2011 11:51:07 +0000 MIME-Version: 1.0 Sent to CCL by: "mirage ." [m.o.m*|*live.fr] --_6c77085a-012b-4f42-8828-93894487d627_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable any help please?? > From: owner-chemistry=-=ccl.net > To: m.o.m=-=live.fr > Subject: CCL: installation of gar2ed > Date: Thu=2C 12 May 2011 14:56:39 -0400 >=20 >=20 > Sent to CCL by: "Serge Lavilier" [m.o.m]=3D[live.fr] > Hi=2C > How to install the gar2ped software in ubuntu 9.04=20 > Thanks >=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=2C please chang= e>=20>=20>=20 > Subscribe/Unsubscribe:=20>=20 > Before posting=2C check wait time at: http://www.ccl.net >=20 > Job: http://www.ccl.net/jobs=20>=20>=20 > If your mail bounces from CCL with 5.7.1 error=2C check:>=20>=20 >=20 = --_6c77085a-012b-4f42-8828-93894487d627_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable any help please??

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= --_6c77085a-012b-4f42-8828-93894487d627_-- From owner-chemistry@ccl.net Fri May 13 08:44:00 2011 From: "Sergio Emanuel Galembeck segalemb!=!usp.br" To: CCL Subject: CCL:G: What's the appropriate method? Message-Id: <-44631-110513084155-23892-gTFjY/jBE/pKXL9RFB0YNA*_*server.ccl.net> X-Original-From: Sergio Emanuel Galembeck Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Fri, 13 May 2011 09:41:42 -0300 MIME-Version: 1.0 Sent to CCL by: Sergio Emanuel Galembeck [segalemb*o*usp.br] Dear Arne, If molecules are not so large, I suggest the use of DFT methods. They are fast and some are reliable. If you could use other programs, I suggest GAMESS, because there are several funcionals, and the EFP2 method for solvation. I only remain that MOPAC2000 is free for academics. Best regards, Sergio Citando "Arne Dieckmann adieckma+*+googlemail.com" : > > Sent to CCL by: Arne Dieckmann [adieckma++googlemail.com] > Thanks, Sergio. Unfortunately, I will have to use Gaussian03 for the > calculations. How about PM3MM then? > > > On May 12, 2011, at 6:00 PM, Sergio Emanuel Galembeck segalemb~~usp.br wrote: > >> >> Sent to CCL by: Sergio Emanuel Galembeck [segalemb-$-usp.br] >> Arne, >> >> I suggest PM6-DH2, present in MOPAC2000. Another option is >> RM1. >> >> Best regards, >> >> Sergio >> >> >> >> >> Citando "Arne Dieckmann adieckma*|*googlemail.com" >> : >> >>> >>> Sent to CCL by: "Arne Dieckmann" [adieckma]*[googlemail.com] >>> Dear all, >>> >>> I would like to optimize some structures containing nucleobases >>> (and base-pairing) as well as peptide-bonds. Furthermore, >>> potentials and barriers for some conformational changes and >>> isomerizations should be determined. I would like to go beyond >>> force fields as the molecules are small enough for e.g. >>> semiempirical methods and use implicit solvation. What >>> semiempirical method (AM1, PM3,...) - if any - would you recommend? >>> >>> >>> Cheers, >>> Arnehttp://www.ccl.net/chemistry/sub_unsub.shtml> >> Job: http://www.ccl.net/jobs> > > From owner-chemistry@ccl.net Fri May 13 18:30:01 2011 From: "Amrita Kumari amrita.g13#%#gmail.com" To: CCL Subject: CCL: Regarding TINKER software Message-Id: <-44632-110513141502-14664-XUQEXHVlfzNF6nv+aLCCkQ-.-server.ccl.net> X-Original-From: "Amrita Kumari" Date: Fri, 13 May 2011 14:15:00 -0400 Sent to CCL by: "Amrita Kumari" [amrita.g13[]gmail.com] Dear all, I am a new user of TINKER software. I have downloaded and installed it on my 32bit Linux system. But I don't know how to check whether it has been installed properly or not. I used command: ./compile.make, ./library.make and ./link.make for installation and it has produced the complete set of TINKER executables. But I don't know how to test this software means how to give input and get output. Thanks, Amrita Kumari Research Scholar IISER Mohali Chandigarh (INDIA).