From owner-chemistry@ccl.net Fri Sep 5 03:51:01 2008 From: "Alexandr Isayev alex[-]ccmsi.us" To: CCL Subject: CCL: ATTN, need revision Message-Id: <-37714-080904165211-13224-W30/KHsYu3Lb8/rvJed+Ng a server.ccl.net> X-Original-From: Alexandr Isayev Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=windows-1251 Date: Thu, 4 Sep 2008 15:01:39 -0500 MIME-Version: 1.0 Sent to CCL by: Alexandr Isayev [alex:_:ccmsi.us] Amine, Did you make sure, you have latest amber ver. Did you applied all bug fixes. Could you please post your PDB file? Without the molecule itself it is really difficult to answer your question. Please also consider to submit this problem to the AMBER mailing list. Thursday, September 4, 2008, 11:57:14 AM, you wrote: aam2hf> Sent to CCL by: "amine amine" [m-22(~)hotmail.fr] aam2hf> Hi aam2hf> I have amber10 and when i run=20 aam2hf> 1/ antechamber -fi pdb -fo prepi -i input.pdb -o output.prepi -c bc= c -at gaff -j 4 aam2hf> 2/ parmchk -i tp.prepin -o tp.frcmod -f prepi -p gaff_parm99m.dat aam2hf> this is my frcmod file aam2hf> ANGLE aam2hf> oh-c3-h1 0.000 0.000 ATTN, need revision aam2hf> oh-c3-c3 0.000 0.000 ATTN, need revision aam2hf> ho-oh-c3 0.000 0.000 ATTN, need revision aam2hf> c3-c3-os 0.000 0.000 ATTN, need revision aam2hf> c3-c3-h1 0.000 0.000 ATTN, need revision aam2hf> c3-c3-c3 0.000 0.000 ATTN, need revision aam2hf> h1-c3-h1 0.000 0.000 ATTN, need revision aam2hf> c3-os-c3 0.000 0.000 ATTN, need revision aam2hf> os-c3-h1 0.000 0.000 ATTN, need revision aam2hf> os-c3-h2 0.000 0.000 ATTN, need revision aam2hf> os-c3-os 0.000 0.000 ATTN, need revision aam2hf> c3-c3-h2 0.000 0.000 ATTN, need revision aam2hf> DIHE aam2hf> oh-c3-c3-os 1 0.000 0.000 0.000 ATTN, n= eed revision aam2hf> oh-c3-c3-h1 1 0.000 0.000 0.000 ATTN, n= eed revision aam2hf> oh-c3-c3-c3 1 0.000 0.000 0.000 ATTN, n= eed revision aam2hf> ho-oh-c3-h1 1 0.000 0.000 0.000 ATTN, n= eed revision aam2hf> ho-oh-c3-c3 1 0.000 0.000 0.000 ATTN, n= eed revision aam2hf> c3-c3-os-c3 1 0.000 0.000 0.000 ATTN, n= eed revision aam2hf> c3-c3-c3-os 1 0.000 0.000 0.000 ATTN, n= eed revision aam2hf> c3-c3-c3-h1 1 0.000 0.000 0.000 ATTN, n= eed revision aam2hf> c3-c3-c3-c3 1 0.000 0.000 0.000 ATTN, n= eed revision aam2hf> h1-c3-c3-os 1 0.000 0.000 0.000 ATTN, n= eed revision aam2hf> h1-c3-c3-h1 1 0.000 0.000 0.000 ATTN, n= eed revision aam2hf> c3-os-c3-h2 1 0.000 0.000 0.000 ATTN, n= eed revision aam2hf> c3-os-c3-os 1 0.000 0.000 0.000 ATTN, n= eed revision aam2hf> os-c3-c3-os 1 0.000 0.000 0.000 ATTN, n= eed revision aam2hf> h1-c3-os-c3 1 0.000 0.000 0.000 ATTN, n= eed revision aam2hf> c3-c3-c3-h2 1 0.000 0.000 0.000 ATTN, n= eed revision aam2hf> oh-c3-c3-oh 1 0.000 0.000 0.000 ATTN, n= eed revision aam2hf> oh-c3-c3-h2 1 0.000 0.000 0.000 ATTN, n= eed revision aam2hf> h1-c3-c3-h2 1 0.000 0.000 0.000 ATTN, n= eed revision aam2hf> IMPROPER aam2hf> NONBON aam2hf> oh 0.0000 0.0000 ATTN, need revision aam2hf> ho 0.0000 0.0000 ATTN, need revision aam2hf> c3 0.0000 0.0000 ATTN, need revision aam2hf> h1 0.0000 0.0000 ATTN, need revision aam2hf> os 0.0000 0.0000 ATTN, need revision aam2hf> h2 0.0000 0.0000 ATTN, need revisio aam2hf> what's wrong?? aam2hf> -=3D This is automatically added to each message by the mailing scr= ipt =3D- aam2hf> To recover the email address of the author of the message, please c= hange aam2hfaam2hfaam2hfaam2hfaam2hfaam2hfaam2hf> Subscribe/Unsubscribe:=20 aam2hfaam2hfaam2hf> Job: http://www.ccl.net/jobs=20 aam2hf> Conferences: aam2hf> http://server.ccl.net/chemistry/announcements/conferences/ aam2hf> Search Messages: http://www.ccl.net/htdig (login: ccl, Password: s= earch) aam2hfaam2hfaam2hf------------------------------------------------------- Alexandr Isayev, Graduate Research Assistant, and System Administrator /./ Computational Center for Molecular Structure and Interactions (CCMSI), Jackson State University, Jackson, MS USA Tel: +(601) 979-1134 e-mail: alex(at)ccmsi.us Web: http://www.ccmsi.us/alex -------------------------------------------------------- From owner-chemistry@ccl.net Fri Sep 5 07:33:01 2008 From: "Jennifer Clare Brookes ucapjcb=ucl.ac.uk" To: CCL Subject: CCL: Advice for funding... Message-Id: <-37715-080905072830-32640-Jr6CyWA3auJTH+yejs2pbw%a%server.ccl.net> X-Original-From: "Jennifer Clare Brookes" Date: Fri, 5 Sep 2008 07:28:25 -0400 Sent to CCL by: "Jennifer Clare Brookes" [ucapjcb]|[ucl.ac.uk] Hi all, I am looking at post-doctoral fellowships for: -An individual with a proposal, from a UK institute, with a physics PhD. -To be held in a UK or USA institute. -An early career scientist (submitting PhD this October). -Within a remit that bridges theoretical physics with biology/ the life-science interface. I have looked around, but for some of the seemingly suitable fellowships I found there have been eligibility issues, or I have come too late in the day. I would really appreciate any guidance/suggestions to what is out there. Any suggestions very welcome -I'd like to exhaust all possibilities. Best wishes, Jenny From owner-chemistry@ccl.net Fri Sep 5 10:32:00 2008 From: "Cesar Augusto Mujica Martinez cesarmujica###gmail.com" To: CCL Subject: CCL: Spectral density for vibrational modes in molecules Message-Id: <-37716-080905102805-15251-GsO9XIiK/B7cjcFGP6J0DQ_._server.ccl.net> X-Original-From: "Cesar Augusto Mujica Martinez" Date: Fri, 5 Sep 2008 10:28:01 -0400 Sent to CCL by: "Cesar Augusto Mujica Martinez" [cesarmujica.(~).gmail.com] Dear CCLers, I have a polymeric molecule in a surface and it is excited by a laser, I am interested in the decay of the excited state (the energy dissipation) and I consider that the mean source of dissipation is the electron-phonon coupling, How can I calculate that electron-phonon coupling? or how to obtain the spectral density function for the vibrational modes given the IR or Raman spectra? Any help or reference is highly appreciated, Thanks in advance, Cesar Mujica cesarmujica(-at-)gmail.com Universidad del Valle Cali, Colombia From owner-chemistry@ccl.net Fri Sep 5 13:54:00 2008 From: "Ramachandran Chelat rcchelat{:}rediffmail.com" To: CCL Subject: CCL: Excited state calculation Message-Id: <-37717-080905134639-4131-mfz0FcwEvghhJ6438YYXrw##server.ccl.net> X-Original-From: "Ramachandran Chelat" Date: Fri, 5 Sep 2008 13:46:35 -0400 Sent to CCL by: "Ramachandran Chelat" [rcchelat]![rediffmail.com] Dear Friends, Can any one tell me which is the largest molecule for which the excited state is calculated and the method and basis set used for that ? Thanking you, Ramachadran From owner-chemistry@ccl.net Fri Sep 5 14:54:01 2008 From: "Mr shabbir shabbir~~nenu.edu.cn" To: CCL Subject: CCL:G: percentage bond character Message-Id: <-37718-080905145304-2912-TKJUA1UeCFFtb7agft0p7g---server.ccl.net> X-Original-From: "Mr shabbir" Date: Fri, 5 Sep 2008 14:53:00 -0400 Sent to CCL by: "Mr shabbir" [shabbir[a]nenu.edu.cn] Dear all This is second time I am puting my problem but still reply missing........I want to calculate the Natural Bond Order: (total/covalent/ionic)using NBO.I am using following keywords in gaussian03 route section pop=nboread gfinput iop(6/7=3) below the molecule specification line $nbo bndidx $end As a result I get Wiberg bond order and some other information but not the (total/covalent/ionic) orders. So any keyword that can give me percentage character of the bond. I would be highly grateful if some one tells me about it. We have also NBO 5 versions but that also I cant use. Regards Mr.Shabbir shabbir(a)nenu.edu.cn From owner-chemistry@ccl.net Fri Sep 5 17:58:00 2008 From: "Scott Brozell srb^osc.edu" To: CCL Subject: CCL: ATTN, need revision Message-Id: <-37719-080905175257-13565-3r3KwIhMrNa76QU7agVLTA(_)server.ccl.net> X-Original-From: Scott Brozell Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Fri, 5 Sep 2008 17:52:43 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: Scott Brozell [srb^osc.edu] Hi, ATTN, need revision indicates a missing force field parameter. The atom types below appear to be normal GAFF, but gaff_parm99m.dat is not a force field parameter file that I recognize. The default force field parameter file (via no -p option) is gaff.dat. If you have further questions then search the Amber mailing list archives before posting to the Amber reflector: http://ambermd.org/ Note the new Amber web site link. Scott On Thu, 4 Sep 2008, Alexandr Isayev alex[-]ccmsi.us wrote: > Sent to CCL by: Alexandr Isayev [alex:_:ccmsi.us] > > Amine, > Did you make sure, you have latest amber ver. Did you applied > all bug fixes. > Could you please post your PDB file? Without the molecule itself > it is really difficult to answer your question. > Please also consider to submit this problem to the AMBER mailing > list. > > Thursday, September 4, 2008, 11:57:14 AM, you wrote: > > aam2hf> Sent to CCL by: "amine amine" [m-22(~)hotmail.fr] > aam2hf> I have amber10 and when i run > > aam2hf> 1/ antechamber -fi pdb -fo prepi -i input.pdb -o output.prepi -c > bcc -at gaff -j 4 > aam2hf> 2/ parmchk -i tp.prepin -o tp.frcmod -f prepi -p gaff_parm99m.dat > aam2hf> this is my frcmod file > > aam2hf> ANGLE > aam2hf> oh-c3-h1 0.000 0.000 ATTN, need revision ... > > aam2hf> DIHE > aam2hf> oh-c3-c3-os 1 0.000 0.000 0.000 ATTN, > need revision ... > aam2hf> IMPROPER > > aam2hf> NONBON > aam2hf> oh 0.0000 0.0000 ATTN, need revision ... From owner-chemistry@ccl.net Fri Sep 5 18:41:00 2008 From: "Nuno A. G. Bandeira nuno.bandeira[#]ist.utl.pt" To: CCL Subject: CCL:G: percentage bond character Message-Id: <-37720-080905183731-737-rkNcuERPBErIcNgvPyaFjg[A]server.ccl.net> X-Original-From: "Nuno A. G. Bandeira" Content-Type: multipart/mixed; boundary="=======AVGMAIL-48C1B4A10000=======" Date: Fri, 05 Sep 2008 23:37:20 +0100 MIME-Version: 1.0 Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira::ist.utl.pt] --=======AVGMAIL-48C1B4A10000======= Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Mr shabbir shabbir~~nenu.edu.cn wrote: > Sent to CCL by: "Mr shabbir" [shabbir[a]nenu.edu.cn] > Dear all > This is second time I am puting my problem but still reply missing........I want to calculate the Natural Bond Order: (total/covalent/ionic)using NBO.I am using > following keywords in gaussian03 route section > pop=nboread gfinput iop(6/7=3) > below the molecule specification line > $nbo bndidx $end > As a result I get Wiberg bond order and some other information but not the > (total/covalent/ionic) orders. So any keyword that can give me percentage > character of the bond. I would be highly grateful if some one tells me about it. > We have also NBO 5 versions but that also I cant use. It sounds like you want to use the NRT routines. NRT is present from NBO 4 onwards. You need to generate a file47 archive from the Gaussian run and then use NBO 5 separately. -- Nuno A. G. Bandeira, AMRSC Graduate researcher and molecular sculptor Inorganic and Theoretical Chemistry Group, Faculty of Science University of Lisbon - C8 building, Campo Grande, 1749-016 Lisbon,Portugal http://cqb.fc.ul.pt/intheochem/nuno.html Doctoral student *_* IST,Lisbon -- --=======AVGMAIL-48C1B4A10000======= Content-Type: multipart/alternative; boundary="=======AVGMAIL-48C1B4A10000=======" --=======AVGMAIL-48C1B4A10000======= Content-Type: text/plain; x-avg=cert; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Content-Description: "AVG certification" No virus found in this outgoing message. Checked by AVG - http://www.avg.com Version: 8.0.169 / Virus Database: 270.6.16/1653 - Release Date: 05-09-2008 = 06:57 --=======AVGMAIL-48C1B4A10000=======-- --=======AVGMAIL-48C1B4A10000=======--