From owner-chemistry@ccl.net Sun Jul 9 05:46:00 2006 From: "=?iso-8859-15?q?=D6d=F6n_Farkas?= farkas(a)chem.elte.hu" To: CCL Subject: CCL:G: freezing atoms without Opt keyword Message-Id: <-32091-060709045436-10194-0jtokRp/jbtQJvYadJjo0Q : server.ccl.net> X-Original-From: =?iso-8859-15?q?=D6d=F6n_Farkas?= Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-15" Date: Sun, 9 Jul 2006 10:53:51 +0200 MIME-Version: 1.0 Sent to CCL by: =?iso-8859-15?q?=D6d=F6n_Farkas?= [farkas ~ chem.elte.hu] Hi Pussana, Use the "Scan:" keyword. More details can be found at: http://www.gaussian.com/g_ur/k_scan.htm Good luck! Ödön On Saturday 08 July 2006 01:49, Pussana Hirunsit Pussana.Hirunsit|*| chemail.tamu.edu wrote: > Sent to CCL by: "Pussana Hirunsit" [Pussana.Hirunsit|chemail.tamu.edu] > Dear All, > I'm using Gaussian program to simulate proton transport in water > clusters. I have fixed the coordinate of 6 water molecules(atom 1- 18) > using keyword Opt=Z-Matrix. I also fix the distance between atom 20 and 23 > and scan the distance between atom 25 and 23. My problem is I want the > program to scan without optimization but if I don't use the keyword > Opt=Z-Matrix, I can't freez atom 1-18 coordinate. Could you suggest me how > to freez atoms' coordinate and scan without performing optimization (only > SCF calculation)? The following is the input file. Thank you for your help. > Best regards, > Pussana > Graudate Student > Texas A&M University > > %chk=Scan_optZ_H14_5WGs.chk > %mem=6MW > %nproc=1 > #p opt=z-matrix b3pw91/6-311++g(d,p) > > Scan H = 14.5, 6 fixed water Gaussian structure > > 1 1 > O 0 A1 B1 C1 > H 0 A2 B2 C2 > H 0 A3 B3 C3 > H 0 A4 B4 C4 > O 0 A5 B5 C5 > H 0 A6 B6 C6 > H 0 A7 B7 C7 > O 0 A8 B8 C8 > H 0 A9 B9 C9 > H 0 A10 B10 C10 > O 0 A11 B11 C11 > H 0 A12 B12 C12 > H 0 A13 B13 C13 > O 0 A14 B14 C14 > H 0 A15 B15 C15 > H 0 A16 B16 C16 > O 0 A17 B17 C17 > H 0 A18 B18 C18 > H 14 E18 11 F17 1 D16 > O 1 E19 5 F18 8 D17 > H 20 E20 1 F19 5 D18 > H 14 E21 11 F20 1 D19 > O 20 E22 1 F21 5 D20 > H 23 E23 5 F22 1 D21 > H 23 E24 5 F23 1 D22 > Variables: > E18 1.38148229 > E19 1.81948165 > E20 0.95988000 > E21 1.39818591 > E23 0.97798322 > E24 0.97821505 S 20 0.05 > F17 92.29566127 > F18 70.24991784 > F19 81.22425202 > F20 138.85801687 > F21 103.16443835 > F22 97.04460806 > F23 129.70631822 > D16 -28.25795916 > D17 82.28508273 > D18 -103.96750943 > D19 -26.55081241 > D20 -17.82012221 > D21 171.42266725 > D22 43.01697243 > Constants: > E22 2.38650760 > A1 6.33352090 > B1 -11.50135061 > C1 -6.95376155 > A2 5.92310099 > B2 -11.59441427 > C2 -7.81646907 > A3 5.60910855 > B3 -11.56976895 > C3 -6.32773016 > A4 5.27412536 > B4 -8.92834151 > C4 -6.11951656 > A5 5.31057625 > B5 -8.41595770 > C5 -6.93038263 > A6 5.45036168 > B6 -7.51065384 > C6 -6.64358204 > A7 4.48628050 > B7 -6.22853083 > C7 -6.76203509 > A8 4.95570918 > B8 -5.39152723 > C8 -6.78280310 > A9 5.52568502 > B9 -5.40959897 > C9 -6.01068227 > A10 5.76195214 > B10 -12.96823713 > C10 -3.85303503 > A11 4.89351810 > B11 -12.81302383 > C11 -4.23132163 > A12 4.81608461 > B12 -11.85786920 > C12 -4.28657840 > A13 4.08182602 > B13 -10.09144478 > C13 -5.37812171 > A14 4.56046487 > B14 -10.17169968 > C14 -4.54997099 > A15 4.52252181 > B15 -9.29642674 > C15 -4.15776287 > A16 3.42247562 > B16 -7.16258216 > C16 -4.20789650 > A17 4.32392982 > B17 -7.48410785 > C17 -4.13460818 > A18 4.80168447 > B18 -6.77899183 > C18 -3.69196669-- Odon Farkas Research Associate Professor Laboratory of Chemical Informatics Institute of Chemistry Eötvös Loránd University, Budapest 1/A Pázmány Péter sétány H-1117 Budapest, Hungary From owner-chemistry@ccl.net Sun Jul 9 09:13:00 2006 From: "Vasileios Tatsis me01136---cc.uoi.gr" To: CCL Subject: CCL: Criterions for the selection of the best peptide mimic Message-Id: <-32092-060709091055-3467-8Kks7DxtXbdZQpTitijxUA]*[server.ccl.net> X-Original-From: "Vasileios Tatsis" Date: Sun, 9 Jul 2006 09:10:43 -0400 Sent to CCL by: "Vasileios Tatsis" [me01136(_)cc.uoi.gr] Dear CCL Members, It is known that the "global" RSMD % value is not always a good criterion for selecting the best peptide in contrast with clusterization of the conformations or the use of adiabatic maps. I would like to pose some questions: 1. "How can I draw these adiabatic maps and then analyze them?" 2. "Also i'd like to know about the clusterization of the conformations". Thanks in advance. Best Regards, Vasilis From owner-chemistry@ccl.net Sun Jul 9 12:01:00 2006 From: "Ross Walker ross{:}rosswalker.co.uk" To: CCL Subject: CCL: Criterions for the selection of the best peptide mimic Message-Id: <-32093-060709115911-25948-9pM+WR8BOeLJOLKh6eneBw!=!server.ccl.net> X-Original-From: "Ross Walker" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Sun, 9 Jul 2006 08:58:45 -0700 MIME-Version: 1.0 Sent to CCL by: "Ross Walker" [ross~~rosswalker.co.uk] Dear Vasileios, The following tutorial contains a section on performing cluster analysis: http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_eight/ All the best Ross /\ \/ |\oss Walker | HPC Consultant and Staff Scientist | | San Diego Supercomputer Center | | Tel: +1 858 822 0854 | EMail:- ross%a%rosswalker.co.uk | | http://www.rosswalker.co.uk | PGP Key available on request | Note: Electronic Mail is not secure, has no guarantee of delivery, may not be read every day, and should not be used for urgent or sensitive issues. > -----Original Message----- > From: owner-chemistry%a%ccl.net [mailto:owner-chemistry%a%ccl.net] > Sent: Sunday, July 09, 2006 08:26 > To: Walker, Ross > Subject: CCL: Criterions for the selection of the best peptide mimic > > Sent to CCL by: "Vasileios Tatsis" [me01136(_)cc.uoi.gr] > Dear CCL Members, > > It is known that the "global" RSMD % value is not always a > good criterion for selecting the best peptide in contrast > with clusterization of the conformations or the use of adiabatic maps. > > I would like to pose some questions: > 1. "How can I draw these adiabatic maps and then analyze them?" > 2. "Also i'd like to know about the clusterization of the > conformations". > > Thanks in advance. > Best Regards, > Vasilis > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, > please change> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, > Password: search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+ > > > >