From owner-chemistry@ccl.net Tue Sep 5 03:22:00 2006 From: "neeraj misra misraneeraj_._gmail.com" To: CCL Subject: CCL: FCARTP Message-Id: <-32479-060905032012-30351-VBCIwZFl8bdCgjoAtKMZsA(-)server.ccl.net> X-Original-From: "neeraj misra" Date: Tue, 5 Sep 2006 03:20:11 -0400 Sent to CCL by: "neeraj misra" [misraneeraj_+_gmail.com] DEAR CCLER'S I SHALL BE THANKFUL IF ANYONE OF YOU COULD SEND ME THE FCARTP SOFTWARE WHICH I NEED BADLY FOR MY NORMAL MODE CALCULATIONS.ANY HELP WOULD BE ACKNOWLEDGED. THANKS IN ADVANCE From owner-chemistry@ccl.net Tue Sep 5 09:32:00 2006 From: "Eric German ernst_german(~)yahoo.com" To: CCL Subject: CCL:G: problem with BSSE Message-Id: <-32480-060904083259-12345-EUHSIZJ0NH8yFYOKuZpMkA*|*server.ccl.net> X-Original-From: Eric German Content-Transfer-Encoding: 8bit Content-Type: multipart/mixed; boundary="0-487934884-1157445730=:15539" Date: Tue, 5 Sep 2006 01:42:10 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Eric German [ernst_german::yahoo.com] --0-487934884-1157445730=:15539 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Content-Id: Content-Disposition: inline Dear friends, I tried to calculate the BSSE in gaussian03. However, I failed to ran my *.com file. Would you please help me. I attach my *.com and *.log files. Many thanks in advance. Eric German, Chemical Engineering Dept, Technion, Haifa __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com --0-487934884-1157445730=:15539 Content-Type: text/plain; name="pdh.dat" Content-Transfer-Encoding: base64 Content-Description: 1558465185-pdh.dat Content-Disposition: attachment; filename="pdh.dat" JWNoaz1wZGgKJU1lbT01MDAwMDAwMAojdGVzdCAgQjNMWVAvR2VuICBQc2V1 ZG89UmVhZCAgU0NGKE1heEN5Y2xlPTE1MCxDb252ZXI9NSkgCklPcCg1LzQ0 PTk5MzAyKSBQT3B0KE1heEN5Y2xlPTEwMCkgIE1hc3NhZ2UKCnBkaCBCU1NF CgowIDEKUGQKSCAgIDEgYQoKYT0xLjUKCjIgTnVjIDAuMCAKCkggMApjYy1w VkRaCioqKioKMSAKTEFOTDJEWgoqKioqCgpQZCAwCkxBTkwyCgogCgoKCg== --0-487934884-1157445730=:15539 Content-Type: text/plain; name="pdh.log" Content-Description: 3164453094-pdh.log Content-Disposition: inline; filename="pdh.log" Entering Gaussian System, Link 0=g03 Initial command: /usr/local/g03/l1.exe /gtmp/Gau-284001.inp -scrdir=/gtmp/ Entering Link 1 = /usr/local/g03/l1.exe PID= 284024. Copyright (c) 1988,1990,1992,1993,1995,1998,2003, Gaussian, Inc. All Rights Reserved. This is the Gaussian(R) 03 program. It is based on the the Gaussian(R) 98 system (copyright 1998, Gaussian, Inc.), the Gaussian(R) 94 system (copyright 1995, Gaussian, Inc.), the Gaussian 92(TM) system (copyright 1992, Gaussian, Inc.), the Gaussian 90(TM) system (copyright 1990, Gaussian, Inc.), the Gaussian 88(TM) system (copyright 1988, Gaussian, Inc.), the Gaussian 86(TM) system (copyright 1986, Carnegie Mellon University), and the Gaussian 82(TM) system (copyright 1983, Carnegie Mellon University). Gaussian is a federally registered trademark of Gaussian, Inc. This software contains proprietary and confidential information, including trade secrets, belonging to Gaussian, Inc. This software is provided under written license and may be used, copied, transmitted, or stored only in accord with that written license. The following legend is applicable only to US Government contracts under DFARS: RESTRICTED RIGHTS LEGEND Use, duplication or disclosure by the US Government is subject to restrictions as set forth in subparagraph (c)(1)(ii) of the Rights in Technical Data and Computer Software clause at DFARS 252.227-7013. Gaussian, Inc. Carnegie Office Park, Building 6, Pittsburgh, PA 15106 USA The following legend is applicable only to US Government contracts under FAR: RESTRICTED RIGHTS LEGEND Use, reproduction and disclosure by the US Government is subject to restrictions as set forth in subparagraph (c) of the Commercial Computer Software - Restricted Rights clause at FAR 52.227-19. Gaussian, Inc. Carnegie Office Park, Building 6, Pittsburgh, PA 15106 USA --------------------------------------------------------------- Warning -- This program may not be used in any manner that competes with the business of Gaussian, Inc. or will provide assistance to any competitor of Gaussian, Inc. The licensee of this program is prohibited from giving any competitor of Gaussian, Inc. access to this program. By using this program, the user acknowledges that Gaussian, Inc. is engaged in the business of creating and licensing software in the field of computational chemistry and represents and warrants to the licensee that it is not a competitor of Gaussian, Inc. and that it will not use this program in any manner prohibited above. --------------------------------------------------------------- Cite this work as: Gaussian 03, Revision B.05, M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, J. A. Montgomery, Jr., T. Vreven, K. N. Kudin, J. C. Burant, J. M. Millam, S. S. Iyengar, J. Tomasi, V. Barone, B. Mennucci, M. Cossi, G. Scalmani, N. Rega, G. A. Petersson, H. Nakatsuji, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, M. Klene, X. Li, J. E. Knox, H. P. Hratchian, J. B. Cross, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, P. Y. Ayala, K. Morokuma, G. A. Voth, P. Salvador, J. J. Dannenberg, V. G. Zakrzewski, S. Dapprich, A. D. Daniels, M. C. Strain, O. Farkas, D. K. Malick, A. D. Rabuck, K. Raghavachari, J. B. Foresman, J. V. Ortiz, Q. Cui, A. G. Baboul, S. Clifford, J. Cioslowski, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham, C. Y. Peng, A. Nanayakkara, M. Challacombe, P. M. W. Gill, B. Johnson, W. Chen, M. W. Wong, C. Gonzalez, and J. A. Pople, Gaussian, Inc., Pittsburgh PA, 2003. ****************************************** Gaussian 03: SGI64-G03RevB.05 8-Nov-2003 5-Sep-2006 ****************************************** %chk=pdh %Mem=50000000 ---------------------------------------------------------------------- #test B3LYP/Gen Pseudo=Read SCF(MaxCycle=150,Conver=5) IOp(5/44=99302) POpt(MaxCycle=100) Massage ---------------------------------------------------------------------- -------- pdh BSSE -------- Symbolic Z-matrix: Charge = 0 Multiplicity = 1 Pd H 1 a Variables: a 1.5 GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Initialization pass. ---------------------------- ! Initial Parameters ! ! (Angstroms and Degrees) ! ---------------------- ---------------------- ! Name Value Derivative information (Atomic Units) ! ------------------------------------------------------------------------ ! a 1.5 estimate D2E/DX2 ! ------------------------------------------------------------------------ Number of steps in this run= 100 maximum allowed number of steps= 100. GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad ------------------------------------------------------------------------ Z-MATRIX (ANGSTROMS AND DEGREES) CD Cent Atom N1 Length/X N2 Alpha/Y N3 Beta/Z J ------------------------------------------------------------------------ 1 1 Pd 2 2 H 1 1.500000( 1) ------------------------------------------------------------------------ Symmetry turned off by external request. Framework group C*V[C*(HPd)] Deg. of freedom 1 Rotational constants (GHZ): 0.0000000 224.9898601 224.9898601 Unrecognized atomic symbol Nuc Error termination via Lnk1e in /usr/local/g03/l301.exe at Tue Sep 5 05:46:32 2006. Job cpu time: 0 days 0 hours 0 minutes 4.1 seconds. File lengths (MBytes): RWF= 13 Int= 0 D2E= 0 Chk= 1 Scr= 1 --0-487934884-1157445730=:15539 Content-Type: text/plain; name="com.txt" Content-Description: 4101646730-com.txt Content-Disposition: inline; filename="com.txt" %chk=pdh %Mem=50000000 #test B3LYP/Gen Pseudo=Read SCF(MaxCycle=150,Conver=5) IOp(5/44=99302) POpt(MaxCycle=100) Massage pdh BSSE 0 1 Pd H 1 a a=1.5 2 Nuc 0.0 H 0 cc-pVDZ **** 1 LANL2DZ **** Pd 0 LANL2 --0-487934884-1157445730=:15539-- From owner-chemistry@ccl.net Tue Sep 5 10:47:01 2006 From: "Tanja van Mourik tanja.vanmourik ~ st-andrews.ac.uk" To: CCL Subject: CCL:G: problem with BSSE Message-Id: <-32481-060905104222-23933-iy2iebYC1nhQ5dP7TPRPiQ]_[server.ccl.net> X-Original-From: Tanja van Mourik Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 05 Sep 2006 15:41:17 +0100 MIME-Version: 1.0 Sent to CCL by: Tanja van Mourik [tanja.vanmourik-$-st-andrews.ac.uk] Hi Eric, > --0-487934884-1157445730=:15539 > Content-Type: text/plain; charset=iso-8859-1 > Content-Transfer-Encoding: 8bit > Content-Id: > Content-Disposition: inline > > Dear friends, > I tried to calculate the BSSE in gaussian03. However, > I failed to ran my *.com file. Would you please help > me. I attach my *.com and *.log files. > Many thanks in advance. I'd propose to use Gaussian's Counterpoise keyword, instead of the old-style Massage. In addition to being much easier to use, the "Counterpoise" option also ensures that proper (matching) integration grid points are used for the ghost atoms. Best wishes, Tanja -- ================================================================= Tanja van Mourik Royal Society University Research Fellow School of Chemistry, University of St. Andrews North Haugh, St. Andrews Fife KY16 9ST, Scotland (UK) email: tanja.vanmourik]_[st-andrews.ac.uk web: http://chemistry.st-and.ac.uk/staffmember.php?id=tvm ================================================================= From owner-chemistry@ccl.net Tue Sep 5 12:22:00 2006 From: "Arvydas Tamulis tamulis+*+mserv.itpa.lt" To: CCL Subject: CCL: What it is the correlation between different ionization potentials Message-Id: <-32482-060905121344-5999-tcVvgveEkyQWMrPBBYS+vQ%%server.ccl.net> X-Original-From: Arvydas Tamulis Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Tue, 5 Sep 2006 19:13:39 +0300 (EEST) MIME-Version: 1.0 Sent to CCL by: Arvydas Tamulis [tamulis_+_mserv.itpa.lt] Dear Colleagues, Usually we obtain quantum mechanically (QM) the ionization potentials which corresponds well with the experimental data of ionization potential of He(I) UV photoelectron (PE) measurements. For example, my last year obtained ionization potential using Koopmans' theorem approximation for guanine is equal to -4.82 eV (calculations were performed with PBEPBE/6-31+G(2p,2d) method). I see that biologists (see example: K. Sugden, B. Martin, Environ Health Perspect. 2002 October; 110(Suppl 5): 725728.) are using data of oxidation potential versus to the normal hydrogen electrode. In this article reference [19] the ionization potential for guanine is equal to -1.29 V. My question is what it is the correlation between values of these two experimental measurements: He(I) UV photoelectron (PE) and oxidation potential versus to the normal hydrogen electrode? How to transform our obtained QM results to the experimentally observed oxidation potential versus to the normal hydrogen electrode? With best regards, Arvydas Tamulis From owner-chemistry@ccl.net Tue Sep 5 12:56:00 2006 From: "Catherine Hayes catherine.hayes=-=nuigalway.ie" To: CCL Subject: CCL: Sterimol software Message-Id: <-32483-060905105830-10510-BVMnNctzzPOJs3IIgpT32A a server.ccl.net> X-Original-From: "Catherine Hayes" Date: Tue, 5 Sep 2006 10:58:29 -0400 Sent to CCL by: "Catherine Hayes" [catherine.hayes=-=nuigalway.ie] Sorry for this probably basic question, but I've read an oldish paper (1986) which mentions using the STERIMOL software. Is this still available, or is there an alternative that people could possibly suggest using? Thanks a million From owner-chemistry@ccl.net Tue Sep 5 13:31:00 2006 From: "Hugo V zquez-Lima monstrilio[a]gmail.com" To: CCL Subject: CCL:G: Troubles whit NBO in Gaussian03 Message-Id: <-32484-060905102016-9685-71ka0UC3iFOIbTJDpLj1Zw[*]server.ccl.net> X-Original-From: "Hugo V zquez-Lima" Date: Tue, 5 Sep 2006 10:20:15 -0400 Sent to CCL by: "Hugo V zquez-Lima" [monstrilio]|[gmail.com] Hello, I have had trouble with some NBO calculations in Gaussian03. I am trying to do a single point job with NBO analysis in which N, O, C, H and Mo atoms appear. I can not get rid of the error "Subroutine NAOANL could not find a S-type core orbital on atom Mo 4". Does anyone have suggestions? INPUT FILE %chk= %mem= %nproc=1 ubhandhlyp/gen 5d pop=(nbo,savenbo) C -0.00000000 -0.00000000 -0.00000000 . From owner-chemistry@ccl.net Tue Sep 5 14:06:00 2006 From: "D.BIO- Gerard Pujadas gerard.pujadas(~)urv.cat" To: CCL Subject: CCL: Is there any 3D-QSAR specialized mailing list? Message-Id: <-32485-060905131700-3019-m6VWmdFjB/aCbWohtgqdOA{:}server.ccl.net> X-Original-From: "D.BIO- Gerard Pujadas" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1; format=flowed Date: Tue, 5 Sep 2006 19:15:29 +0200 Mime-Version: 1.0 Sent to CCL by: "D.BIO- Gerard Pujadas" [gerard.pujadas[-]urv.cat] Dear CCL list subscribers, I wonder if there is a mailing list speciallized in 3D-QSAR Thanks for your help Yours sincerely Gerard -- ============================= NOTE: NEW E-MAIL ============================ Dr. Gerard Pujadas Grup de recerca en Nutrigenòmica Dept. Bioquímica i Biotecnologia room 106 Campus de Sant Pere Sescelades e-mail: gerard.pujadas++urv.cat Univ. Rovira i Virgili phone: 34-977 559565 C/ Marcel·lí Domingo fax: 34-977 558232 43007 Tarragona (CATALONIA) State: Spain (European Union) =========================================================================== From owner-chemistry@ccl.net Tue Sep 5 14:42:00 2006 From: "Steve Bowlus chezbowlus : goldrush.com" To: CCL Subject: CCL: Sterimol software Message-Id: <-32486-060905143158-31885-eXeb3Gw0lzi/L5RyWD4DFw#server.ccl.net> X-Original-From: Steve Bowlus Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 05 Sep 2006 11:31:18 -0700 MIME-Version: 1.0 Sent to CCL by: Steve Bowlus [chezbowlus[]goldrush.com] Sterimol was deposited with QCPE in 1994 or thereabouts. So contact QCPE or Indiana University chem department for an official version. Or you might try other repositories (CCL?) in the off-chance that other users have uploaded the code. I have found the documentation, but the program itself seems to have been trashed at some point. I may still have it archived somewhere, but you will need to be patient while I search ... with no guarantee of success. Cheers, Steve Catherine Hayes catherine.hayes=-=nuigalway.ie wrote: > Sent to CCL by: "Catherine Hayes" [catherine.hayes=-=nuigalway.ie] > Sorry for this probably basic question, but I've read an oldish paper (1986) which mentions using the STERIMOL software. Is this still available, or is there an alternative that people could possibly suggest using? > > Thanks a million From owner-chemistry@ccl.net Tue Sep 5 15:34:01 2006 From: "Johanna Jansen hanneke_jansen_-_chiron.com" To: CCL Subject: CCL: COMP: ACS Fall meeting program & opportunity for a free copy of ARCC-1 Message-Id: <-32487-060905153135-3181-ZDaXArFlIDjoaK3DbWvrNw%server.ccl.net> X-Original-From: "Johanna Jansen" Date: Tue, 5 Sep 2006 15:31:35 -0400 Sent to CCL by: "Johanna Jansen" [hanneke_jansen{:}chiron.com] Dear COMP members and colleagues interested in becoming COMP members, The Executive Committee of the Computers in Chemistry division (COMP) of the ACS is very excited to see yet another excellent program being presented for the upcoming Fall meeting in San Francisco, September 10-14, by our programming chair and co-chair, Wendy Cornell and Jeffry Madura. We would like to remind you that the program details for this meeting are available on our website at http://membership.acs.org/C/COMP/program.html We look forward to seeing our existing and potential new members at the meeting. We would like to especially welcome you to the poster session on Tuesday evening. As an additional incentive, we are offering a free copy of the first volume of the Annual Reports in Computational Chemistry (ARCC) to the first 25 people who present the coupon available from the COMP website http://membership.acs.org/C/COMP/ at that poster session. Only one coupon per person! Annual Reports in Computational Chemistry (ARCC) is a periodical providing timely and critical reviews of important topics in computational chemistry as applied to all chemical disciplines. This book is being provided as a COMP membership benefit. The first volume was published in 2005, and the second volume is coming out in the next few months. Volume 2 will be distributed to all members in good standing according to the 2005 year-end membership list for the COMP division. We encourage all members and interested colleagues to sign up for the COMP Division and make sure their membership is in good standing by year-end 2006 to ensure their place on the mailing list for volume 3, coming in 2007. We're hoping to see you in San Francisco! For the Executive Committee, Hanneke Jansen, Secretary From owner-chemistry@ccl.net Tue Sep 5 16:51:01 2006 From: "Rick Venable rvenable]=[pollux.cber.nih.gov" To: CCL Subject: CCL: Sterimol software Message-Id: <-32488-060905144346-4573-HXerKBiV3iM/d7r9fmxGPg()server.ccl.net> X-Original-From: Rick Venable Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Tue, 5 Sep 2006 13:45:36 -0400 MIME-Version: 1.0 Sent to CCL by: Rick Venable [rvenable__pollux.cber.nih.gov] On Tue, 5 Sep 2006, Catherine Hayes catherine.hayes=-=nuigalway.ie wrote: > Sorry for this probably basic question, but I've read an oldish paper > (1986) which mentions using the STERIMOL software. Is this still > available, or is there an alternative that people could possibly > suggest using? STERIMOL appears to be a group of shape based QSAR descriptors introduced by Verloop which a number of programs can compute, such as ChemDraw, as well as a QCPE offering. ------------------------------------- Rick Venable 29/500 Membrane Biophysics Section NIH/NHLBI Lab. of Comp. Biology Bethesda, MD 20892-8014 U.S.A. (301) 496-1905 Rick_Venable AT nih*gov ALT email: rvenable AT speakeasy*org ------------------------------------- From owner-chemistry@ccl.net Tue Sep 5 17:48:00 2006 From: "Anil Aron anisamron . yahoo.com" To: CCL Subject: CCL: Fermi resonance & Vib spectroscopy Message-Id: <-32489-060904185506-18044-vOf0L9Gpg7jf8YS+wOtYYw]*[server.ccl.net> X-Original-From: Anil Aron Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1943192406-1157406899=:47768" Date: Mon, 4 Sep 2006 22:54:59 +0100 (BST) MIME-Version: 1.0 Sent to CCL by: Anil Aron [anisamron|a|yahoo.com] --0-1943192406-1157406899=:47768 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hello There, I am basically from biology student and doing my Masters. I am not well versed with spectroscopy & theory and in the process of learning. I am doing some vibrational calculations and I have couple of fundamental doubts. 1) I would like to know how to assign the vibrations to the frequency from theoretical data. I mean, how do I give the n1, n2, n3, …. corresponding each frequency? (neu1, neu2, etc,) 2) About Fermi resonances. How do I select the bands/modes which form the Fermi resonance. Also could you any one of you suggest some online materials to read/ OR From where (books) to get some information related to these? I would really appreciate any feedback from you. I guess some one in this list has asked questions similar to what I like. Thanks, Regards, Aron Send instant messages to your online friends http://uk.messenger.yahoo.com --0-1943192406-1157406899=:47768 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Hello There,
I am basically from biology student and doing my Masters. I am not well versed with spectroscopy & theory and in the process of learning.
 
I am doing some vibrational calculations and I have couple of fundamental doubts.
 
1) I would like to know how to assign the vibrations to the frequency from theoretical data. I mean, how do I give the n1, n2,  n3,  …. corresponding each frequency? (neu1, neu2, etc,)
 
2) About Fermi resonances. How do I select the bands/modes which form the Fermi resonance.
 
Also could you any one of you suggest some online materials to read/ OR From where (books) to get some information related to these? I would really appreciate any feedback from you.
 
I guess some one in this list has asked questions similar to what I like.
 
 
 
Thanks,
Regards,
Aron

Send instant messages to your online friends http://uk.messenger.yahoo.com --0-1943192406-1157406899=:47768-- From owner-chemistry@ccl.net Tue Sep 5 18:22:00 2006 From: "Yubo Fan yubofan__mail.chem.tamu.edu" To: CCL Subject: CCL: umbrella sampling using amber 8/9 Message-Id: <-32490-060904215317-9015-pZU31dnbQER9LD3vfBYgSQ*_*server.ccl.net> X-Original-From: "Yubo Fan" Content-Type: multipart/alternative; boundary="----=_NextPart_000_000B_01C6D05B.BA958400" Date: Mon, 4 Sep 2006 19:53:01 -0500 MIME-Version: 1.0 Sent to CCL by: "Yubo Fan" [yubofan%%mail.chem.tamu.edu] This is a multi-part message in MIME format. ------=_NextPart_000_000B_01C6D05B.BA958400 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi, everyone, I am trying to analyze the reaction coordinate using umbrella sampling. = What I want to do is to get the free energy along the reaction coordiate = for ammonia transfer in a protein. This method is not very well = documented in Amber's manual. Is there any similar example available? Or = any advice. Thanks in advance. Sincerely, Yubo =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=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 Dr. Yubo Fan Email: yubofan,+,mail.chem.tamu.edu Department of Chemistry Tel: 1-979-845-5237 Texas A&M University College Station, TX 77843 =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=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 ------=_NextPart_000_000B_01C6D05B.BA958400 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Hi, everyone,
 
I am trying to analyze the reaction = coordinate=20 using umbrella sampling. What I want to do is to get the free energy = along the=20 reaction coordiate for ammonia transfer in a protein. This method is not = very=20 well documented in Amber's manual. Is there any similar example = available? Or=20 any advice. Thanks in advance.
 
Sincerely,
 
Yubo
=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=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
Dr. Yubo=20 Fan           &nbs= p;  =20 Email: yubofan,+,mail.chem.tamu.edu=
Department=20 of Chemistry    Tel:   1-979-845-5237
Texas = A&M=20 University
College Station, TX=20 77843
=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=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
------=_NextPart_000_000B_01C6D05B.BA958400--