From chemistry-request@server.ccl.net Thu Feb 28 03:18:26 2002 Received: from smtp2.ruc.dk ([130.225.220.70]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1S8IP525641 for ; Thu, 28 Feb 2002 03:18:25 -0500 Received: by smtp2.ruc.dk (Postfix, from userid 504) id D05681942CD; Thu, 28 Feb 2002 09:17:56 +0100 (CET) Received: from smtprelay.ruc.dk (smtprelay.ruc.dk [130.225.220.22]) by smtp2.ruc.dk (Postfix) with ESMTP id A78CE1942CA; Thu, 28 Feb 2002 09:17:55 +0100 (CET) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtprelay.ruc.dk (8.9.3+Sun/8.9.3) with ESMTP id IAA12652; Thu, 28 Feb 2002 08:48:28 +0100 (MET) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.47); 28 Feb 02 09:17:54 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.47); 28 Feb 02 09:17:51 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: "Students of Dr. S. R. Gadre" Date: Thu, 28 Feb 2002 09:17:35 +0100 Subject: CCL: Correlation effect on .... Reply-To: spanget@ruc.dk Cc: chemistry@ccl.net Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: <717C4917DCD@virgil.ruc.dk> "Students of Dr. S. R. Gadre": > CCLer's... > Could somebody give me a concrete example of weakly interacting > geometrical conformers where the energy trends reverse in correlated > methods.( One of the weakly interacting geometrical conformers which > was a lower energy minimum at Hartree Fock level should not be a > lower energy minimum in a correlated method like MP2 ...a conformer > which was not a lower energy minimum in Hartree Fock becoming a > lower energy minimum with a correlated method is the kind of > situation that i am looking for...the structures should be > stationary points on the PES) Dear Bala, the example of 1,6,6a-trithiapentalene may be of interest to you. Ab initio Hartree-Fock theory predicts an equilibrium geometry of Cs molecular symmetry, corresponding to a situation with two equivalent Cs symmetrical valence tautomers separated by a barrier of about 10 kcal/mol. Introduction of electron correlation effects (MP2, DFT) leads to the prediction of a single C2v symmetrical equilibrium geometry, consistent with the experimental evidence: K. B. Andersen, J. Abildgaard, J. G. Radziszewski, J. Spanget-Larsen, J. Phys. Chem. A 101, 4475 (1997) J. Spanget-Larsen, K. B. Andersen, Phys. Chem. Chem. Phys. 3, 908 (2001) Yours, Jens >--< NB! Please note new mail address: =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Office: +45 4674 2710 Department of Chemistry Fax: +45 4674 3011 Roskilde University (RUC) Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget@ruc.dk DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~spanget =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@server.ccl.net Thu Feb 28 02:32:40 2002 Received: from krf.reac.chem.t.u-tokyo.ac.jp ([133.11.173.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1S7Wd524612; Thu, 28 Feb 2002 02:32:39 -0500 Received: from ye (dhcp113.reac.chem.t.u-tokyo.ac.jp [192.168.1.113]) by krf.reac.chem.t.u-tokyo.ac.jp (8.9.3/3.7Wpl2) with SMTP id QAA04782; Thu, 28 Feb 2002 16:18:04 +0900 Message-ID: <001c01c1c02a$18fbd040$7101a8c0@reac.chem.t.utokyo.ac.jp> From: "Shuji Ye" To: Cc: Subject: Would you like to help me? Date: Thu, 28 Feb 2002 16:32:37 +0900 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0018_01C1C075.88BA4560" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 This is a multi-part message in MIME format. ------=_NextPart_000_0018_01C1C075.88BA4560 Content-Type: text/plain; charset="iso-2022-jp" Content-Transfer-Encoding: 7bit Dear everyone, I am a new learner of Gaussian 98. I have a difficulty in calculating the force constants of larger molecules using Gaussian 98. Though I can get the force constants for every mode in the infrared spectra, I don't know how to transfer these constants into bond stretching, angle bending and torsional force constants. For example, I can get the following informations of the calculation of nitrate ion NO3(-1) at B3LYP/6-311G(d) level. I want to know the force constants of bond stretching N-O and angle bending O-N-O and torsional moting O-N-O-O.( The intramolecular interaction potential has the form V(intra)=V(stretch)+V(bend)+V(torsion). V(stretch)=1/2Kr(r-r0)^2, V(bend)=1/2Ktheta(theta-theta0)^2, V(torsion)=Kphi(1-icos(2phi-phi0)) If you know how to do it or you are good at using Gaussian 98, would you like to give me any advice? It is appreciated for your kind help. Sincerely yours Shuji Ye ------------------------------- Shuji Ye Depertment of Chemical System Engineering, Graduate School of Engineering The University of Tokyo 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan -------------------------------- Raman scattering activities (A**4/AMU), Raman depolarization ratios, reduced masses (AMU), force constants (mDyne/A) and normal coordinates: 1 2 3 A1 B2 B1 Frequencies -- 716.4176 716.7829 844.0095 Red. masses -- 15.8585 15.8583 14.4084 Frc consts -- 4.7956 4.8004 6.0473 IR Inten -- 0.5951 0.6005 23.6155 Raman Activ -- 0.0000 0.0000 0.0000 Depolar -- 0.0000 0.0000 0.0000 Atom AN X Y Z X Y Z X Y Z 1 7 0.00 0.00 0.26 0.00 -0.26 0.00 0.89 0.00 0.00 2 8 0.00 0.00 0.48 0.00 0.63 0.00 -0.26 0.00 0.00 3 8 0.00 -0.48 -0.35 0.00 -0.20 0.48 -0.26 0.00 0.00 4 8 0.00 0.48 -0.35 0.00 -0.20 -0.48 -0.26 0.00 0.00 4 5 6 A1 A1 B2 Frequencies -- 1068.1719 1431.6263 1431.6450 Red. masses -- 15.9949 14.5209 14.5211 Frc consts -- 10.7526 17.5350 17.5356 IR Inten -- 0.0003 498.8348 498.9929 Raman Activ -- 0.0000 0.0000 0.0000 Depolar -- 0.0000 0.0000 0.0000 Atom AN X Y Z X Y Z X Y Z 1 7 0.00 0.00 0.00 0.00 0.00 0.86 0.00 0.86 0.00 2 8 0.00 0.00 0.58 0.00 0.00 -0.40 0.00 -0.10 0.00 3 8 0.00 0.50 -0.29 0.00 0.13 -0.17 0.00 -0.33 0.13 4 8 0.00 -0.50 -0.29 0.00 -0.13 -0.17 0.00 -0.33 -0.13 ------=_NextPart_000_0018_01C1C075.88BA4560 Content-Type: text/html; charset="iso-2022-jp" Content-Transfer-Encoding: quoted-printable
Dear everyone,

 I am a new learner of = Gaussian=20 98.  I have a difficulty in calculating the force constants of = larger=20 molecules
using Gaussian 98. Though I can get the force constants for = every=20 mode in the infrared spectra, I don't know how to transfer these = constants=20 into
bond stretching, angle bending and torsional force = constants.=20 For example, I can get the following informations of the calculation of = nitrate=20 ion NO3(-1) at B3LYP/6-311G(d) level. I want to know the force constants = of bond=20 stretching N-O and angle bending O-N-O and torsional moting = O-N-O-O.( The=20 intramolecular interaction potential has the form=20 V(intra)=3DV(stretch)+V(bend)+V(torsion). V(stretch)=3D1/2Kr(r-r0)^2, =
V(bend)=3D1/2Ktheta(theta-theta0)^2,=20 V(torsion)=3DKphi(1-icos(2phi-phi0))

If you know how to do it or = you are=20 good at using Gaussian 98, would you like to give me any advice?
It = is=20 appreciated for  your kind help.

 Sincerely=20 yours

 Shuji = Ye
 -------------------------------
Shuji Ye

Depertment of Chemical System Engineering,
Graduate School of Engineering
The University of Tokyo
7-3-1 = Hongo,=20 Bunkyo-ku, Tokyo 113-8656, Japan
 --------------------------------

  Raman = scattering=20 activities (A**4/AMU), Raman depolarization ratios,
  reduced = masses=20 (AMU), force constants (mDyne/A) and normal=20 coordinates:
         &nb= sp;           =20 1            =          =20 2            =          =20 3
           &n= bsp;        =20 A1            = ;        =20 B2            = ;        =20 B1
  Frequencies --  =20 716.4176           = ;   =20 716.7829           = ;   =20 844.0095
  Red. masses --   =20 15.8585           =     =20 15.8583           =     =20 14.4084
  Frc consts  --    =20 4.7956           &= nbsp;    =20 4.8004           &= nbsp;    =20 6.0473
  IR Inten    --    =20 0.5951           &= nbsp;    =20 0.6005           &= nbsp;   =20 23.6155
  Raman Activ --    =20 0.0000           &= nbsp;    =20 0.0000           &= nbsp;    =20 0.0000
  Depolar     = --    =20 0.0000           &= nbsp;    =20 0.0000           &= nbsp;    =20 0.0000
  Atom AN     =20 X      Y     =20 Z        = X     =20 Y      = Z       =20 X      Y     =20 Z
    1   7     = 0.00  =20 0.00   0.26     0.00  = -0.26  =20 0.00     0.89   0.00 = 0.00
   =20 2   8     0.00   = 0.00  =20 0.48     0.00   0.63  =20 0.00    -0.26   0.00 0.00
    = 3   8     0.00  -0.48 =20 -0.35     0.00  -0.20  =20 0.48    -0.26   0.00 0.00
    = 4   8     0.00   0.48 =20 -0.35     0.00  -0.20  = -0.48   =20 -0.26   0.00=20 0.00
           = ;          =20 4            =          =20 5            =          =20 6
           &n= bsp;       =20 A1            = ;        =20 A1            = ;        =20 B2
  Frequencies -- =20 1068.1719          &nbs= p;  =20 1431.6263          &nbs= p;  =20 1431.6450
  Red. masses --   =20 15.9949           =     =20 14.5209           =     =20 14.5211
  Frc consts  --   =20 10.7526           =     =20 17.5350           =     =20 17.5356
  IR Inten    --    =20 0.0003           &= nbsp;  =20 498.8348           = ;   =20 498.9929
  Raman Activ --    =20 0.0000           &= nbsp;    =20 0.0000           &= nbsp;    =20 0.0000
  Depolar     = --    =20 0.0000           &= nbsp;    =20 0.0000           &= nbsp;    =20 0.0000
  Atom AN     =20 X      Y     =20 Z        = X     =20 Y      = Z       =20 X      Y     =20 Z
    1   7     = 0.00  =20 0.00   0.00     0.00   = 0.00  =20 0.86     0.00   0.86 = 0.00
   =20 2   8     0.00   = 0.00  =20 0.58     0.00   0.00 =20 -0.40     0.00  -0.10 = 0.00
   =20 3   8     0.00   0.50 =20 -0.29     0.00   0.13 =20 -0.17     0.00  -0.33 = 0.13
   =20 4   8     0.00  -0.50 =20 -0.29     0.00  -0.13  -0.17  =20 0.00  -0.33  -0.13



 ------=_NextPart_000_0018_01C1C075.88BA4560-- From chemistry-request@server.ccl.net Thu Feb 28 05:00:01 2002 Received: from ns1.tudelft.nl ([130.161.180.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1SA01527614 for ; Thu, 28 Feb 2002 05:00:01 -0500 Received: from CONVERSION-DAEMON.mailhost2.tudelft.nl by mailhost2.tudelft.nl (PMDF V6.1 #40925) id <0GS800L01MF2WY@mailhost2.tudelft.nl> for chemistry@ccl.net; Thu, 28 Feb 2002 10:59:28 +0100 (MET) Received: from listserv.tudelft.nl (listserv.tudelft.nl [130.161.180.33]) by mailhost2.tudelft.nl (PMDF V6.1 #40925) with ESMTP id <0GS800L43MF2CP@mailhost2.tudelft.nl> for chemistry@ccl.net; Thu, 28 Feb 2002 10:59:26 +0100 (MET) Received: from stm-ltc2.dct.tudelft.nl (stm-ltc2.dct.tudelft.nl [130.161.196.198]) by listserv.tudelft.nl (8.10.2+Sun/8.10.2) with ESMTP id g1S9xP525415 for ; Thu, 28 Feb 2002 10:59:25 +0100 (MET) Received: from STM-LTC2/SpoolDir by stm-ltc2.dct.tudelft.nl (Mercury 1.47) ; Thu, 28 Feb 2002 10:59:25 +0000 (MET-1MEST) Received: from SpoolDir by STM-LTC2 (Mercury 1.47); Thu, 28 Feb 2002 10:59:23 +0000 (MET-1MEST) Date: Thu, 28 Feb 2002 10:59:20 +0100 From: Martijn Zwijnenburg Subject: semi-emperical molecular dynamics To: chemistry@ccl.net Message-id: <3C7E0D88.18648.41A520F@localhost> MIME-version: 1.0 X-Mailer: Pegasus Mail for Win32 (v3.12c) Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Priority: normal Hi, Does anybody know, if there exist packages to do molecular dynamics using semi-empirical hamiltonians (AM1, PM3)? cheers, Martijn ------------------------------------------------------------------------- Martijn Zwijnenburg Lab. of Applied Organic Chemistry and Catalysis Delft University of Technology Julianalaan 136 2628 BL Delft The Netherlands Tel: 0031-(0)152782691 Fax: 0031-(0)152784700 e-mail: M.A.Zwijnenburg@tnw.tudelft.nl web page: http://come.to/tock From chemistry-request@server.ccl.net Thu Feb 28 06:13:36 2002 Received: from artemis.le.ac.uk ([143.210.16.126]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1SBDa528781 for ; Thu, 28 Feb 2002 06:13:36 -0500 Received: from owl.le.ac.uk ([143.210.8.54]) by artemis.le.ac.uk with esmtp (Exim 3.16 #1) id 16gOUn-00030o-00 for chemistry@ccl.net; Thu, 28 Feb 2002 11:13:09 +0000 Date: Thu, 28 Feb 2002 11:13:12 +0000 (GMT) From: Stewart Kirton X-Sender: sbk1@owl To: chemistry@ccl.net Subject: QXP Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello to all at ccl, I am intrigued by the capabilities of QXP with regards to docking of small molecules into a flexible active site. Could someone please tell me who I would need to contact to find out more about the Flo99 software - and whether or not there is an academic version available? Also, comments on how you have found QXP to cope (particularly with haem-containing proteins) would be gratefully received. Many thanks and best wishes Stewart ------------------------------------------------------------------------------- Stewart Kirton |e-mail: sbk1@le.ac.uk Dept. Chemistry | University of Leicester | University Road | Leicester | LE1 7RH | Tel: (0116) 2523620 | ------------------------------------------------------------------------------- From chemistry-request@server.ccl.net Thu Feb 28 06:32:59 2002 Received: from igcar.ernet.in ([202.141.82.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1SBWT529047 for ; Thu, 28 Feb 2002 06:32:59 -0500 Received: from igcar.ernet.in (localhost.localdomain [127.0.0.1]) by igcar.ernet.in (8.9.3/8.9.3) with ESMTP id RAA03766 for ; Thu, 28 Feb 2002 17:05:54 +0530 Received: from [203.199.205.25] ([203.199.205.25]) by igcar.ernet.in (8.9.3/8.9.3) with SMTP id RAA03758 for ; Thu, 28 Feb 2002 17:05:53 +0530 Received: from [10.1.1.100] by [203.199.205.25] via smtpd (for igcar.ernet.in [202.141.82.2]) with SMTP; 28 Feb 2002 11:33:03 UT Received: (from Urcl@localhost) by igcmail.igcar.ernet.in (8.9.3+Sun/8.9.1) id RAA14562 for chemistry@www.ccl.net; Thu, 28 Feb 2002 17:03:13 -0500 (GMT) X-Authentication-Warning: igcmail.igcar.ernet.in: Urcl set sender to vvenkat@igcar.ernet.in using -f >Received: from localhost by rcl.igcar.ernet.in (8.9.1b+Sun/SMI-SVR4) id RAA23290; Thu, 28 Feb 2002 17:01:08 -0500 (GMT) Date: Thu, 28 Feb 2002 17:01:08 -0500 (GMT) From: "V.Venkatesan" X-Sender: vvenkat@rcl To: chemistry@server.ccl.net Subject: bond order calculation from aimpac Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII HELLO FROM AIMPAC, IS IT POSSIBLE TO CALCULATE THE BOND ORDER? PLEASE GIVE REPLY ******************************************************************************* NAME:V.VENKATESAN ADDRESS:MATERIALS CHEMISTRY DIVISION RADIOCHEMICAL LABORATORY INDIRA GANDHI CENTRE FOR ATOMIC RESEACH KALPAKKAM-603102 TAMILNADU INDIA E-MAIL ID:vvenkat@igcar.ernet.in ******************************************************************************* From chemistry-request@server.ccl.net Thu Feb 28 07:51:33 2002 Received: from mmb1.vsnl.net.in ([202.54.1.72]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1SCpX529876 for ; Thu, 28 Feb 2002 07:51:33 -0500 Received: from bom2.vsnl.net.in (unknown [203.199.88.20]) by mmb1.vsnl.net.in (Postfix) with ESMTP id 1345E547C9 for ; Thu, 28 Feb 2002 18:20:52 +0530 (IST) Message-ID: <3C7E2511.9AF7ABB1@bom2.vsnl.net.in> Date: Thu, 28 Feb 2002 18:09:45 +0530 From: meenatul X-Mailer: Mozilla 4.7 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: CCL Subject: azodye X-Priority: 1 (Highest) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear All I would like to know about an analytical method which will distinguish between bromo substituted azodye from choloro substituted azodye (Br/Cl are at para position and rest of the substitutions are identical in both compounds). What are the frequencies or the specific requirements, which will give the proper difference between these two compounds? Thanks Meena From chemistry-request@server.ccl.net Thu Feb 28 09:13:18 2002 Received: from ns1.tudelft.nl ([130.161.180.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1SEDI530789 for ; Thu, 28 Feb 2002 09:13:18 -0500 Received: from CONVERSION-DAEMON.mailhost2.tudelft.nl by mailhost2.tudelft.nl (PMDF V6.1 #40925) id <0GS800B01Y5CAU@mailhost2.tudelft.nl> for chemistry@ccl.net; Thu, 28 Feb 2002 15:12:50 +0100 (MET) Received: from listserv.tudelft.nl (listserv.tudelft.nl [130.161.180.33]) by mailhost2.tudelft.nl (PMDF V6.1 #40925) with ESMTP id <0GS8002MEY5BIH@mailhost2.tudelft.nl> for chemistry@ccl.net; Thu, 28 Feb 2002 15:12:48 +0100 (MET) Received: from stm-ltc2.dct.tudelft.nl (stm-ltc2.dct.tudelft.nl [130.161.196.198]) by listserv.tudelft.nl (8.10.2+Sun/8.10.2) with ESMTP id g1SECl518154 for ; Thu, 28 Feb 2002 15:12:47 +0100 (MET) Received: from STM-LTC2/SpoolDir by stm-ltc2.dct.tudelft.nl (Mercury 1.47) ; Thu, 28 Feb 2002 15:12:47 +0000 (MET-1MEST) Received: from SpoolDir by STM-LTC2 (Mercury 1.47); Thu, 28 Feb 2002 15:12:47 +0000 (MET-1MEST) Date: Thu, 28 Feb 2002 15:12:44 +0100 From: Martijn Zwijnenburg Subject: experience with semi-empirical MD To: chemistry@ccl.net Message-id: <3C7E48F2.14442.60AED57@localhost> MIME-version: 1.0 X-Mailer: Pegasus Mail for Win32 (v3.12c) Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Priority: normal Hi, Several people told me, in a reply to my question, that it's possible to do semi-empirical molecular dynamics (AM1, PM3) with Hyperchem, Mopac and Spartan. Now I wonder if somebody can give me some practical information on systems one can treat on a state of the art linux or windows 2000 machine. I know this is not something fixed and depends on how long one is willing to wait for the simulation to finish but I just want to get some feeling. Any experience, especially with solution systems, is more then welcome. Cheers Martijn ------------------------------------------------------------------------- Martijn Zwijnenburg Lab. of Applied Organic Chemistry and Catalysis Delft University of Technology Julianalaan 136 2628 BL Delft The Netherlands Tel: 0031-(0)152782691 Fax: 0031-(0)152784700 e-mail: M.A.Zwijnenburg@tnw.tudelft.nl web page: http://come.to/tock From chemistry-request@server.ccl.net Thu Feb 28 10:49:11 2002 Received: from soul.helsinki.fi ([128.214.3.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1SFnA532256 for ; Thu, 28 Feb 2002 10:49:11 -0500 Received: from localhost (sundius@localhost) by soul.helsinki.fi (8.9.3/8.9.3) with ESMTP id RAA12586; Thu, 28 Feb 2002 17:48:07 +0200 (EET) X-Authentication-Warning: soul.helsinki.fi: sundius owned process doing -bs Date: Thu, 28 Feb 2002 17:48:07 +0200 (EET) From: Tom Sundius X-Sender: To: Shuji Ye cc: , =?ISO-8859-1?Q?Kim_Palm=F6?= Subject: Re: CCL:Would you like to help me? In-Reply-To: <001c01c1c02a$18fbd040$7101a8c0@reac.chem.t.utokyo.ac.jp> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 28 Feb 2002, Shuji Ye wrote: > Dear everyone, > > I am a new learner of Gaussian 98. I have a difficulty in calculating the > force constants of larger molecules > using Gaussian 98. Though I can get the force constants for every mode in > the infrared spectra, I don't know how to transfer these constants into > bond stretching, angle bending and torsional force constants. For example, I > can get the following informations of the calculation of nitrate ion NO3(-1) > at B3LYP/6-311G(d) level. I want to know the force constants of bond > stretching N-O and angle bending O-N-O and torsional moting O-N-O-O.( The > intramolecular interaction potential has the form > V(intra)=V(stretch)+V(bend)+V(torsion). V(stretch)=1/2Kr(r-r0)^2, > V(bend)=1/2Ktheta(theta-theta0)^2, V(torsion)=Kphi(1-icos(2phi-phi0)) > > If you know how to do it or you are good at using Gaussian 98, would you > like to give me any advice? > It is appreciated for your kind help. You cannot use Gaussian to transform an ab initio force field directly to internal coordinates. But you can read the ab initio cartesian force field > from the archive part of the output, or the checkpoint file (after you have converted it from binary to ASCII) and input it to a normal coordinate analysis program and then convert the ab initio force field to internal coordinates or symmetry coordinates. If you really want to calculate a molecular mechanics force field from the ab initio force field, it is more complicated, but can be done (see, for instance, K. Palmo, L-O Pietila and S. Krimm, J. Comput. Chem. 12, 385 (1991)). Greetings, Tom Sundius Tom Sundius University of Helsinki, Dept of Physical Sciences phone +358-9-191 50672 P.O.Box 64, FIN-00014 Helsinki, Finland fax +358-9-191 50610 From chemistry-request@server.ccl.net Thu Feb 28 11:54:40 2002 Received: from aspirine.u-strasbg.fr (IDENT:root@[130.79.84.250]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1SGse500707 for ; Thu, 28 Feb 2002 11:54:40 -0500 Received: from hit4 (lead2.u-strasbg.fr [130.79.85.21]) by aspirine.u-strasbg.fr (8.10.2/8.10.2) with ESMTP id g1SGP2E13777 for ; Thu, 28 Feb 2002 17:25:02 +0100 From: "Logean Antoine" To: Subject: A little geometrical problem Date: Thu, 28 Feb 2002 17:43:41 +0100 Message-ID: <000e01c1c077$1751e9d0$2d554f82@hit4> MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2627 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2526.0000 Importance: Normal A little geometrical problem : Taken a residue in a PDB file, how can I calculate the Cartesian coordinates of CB when I know the coordinates of N, CA and C, the angle N-CA-CB, C-CA-CB and the bond length CA-CB ? It seems to be trivial but I am unable to find a solution ! I am sure that somebody can help me. In advance thank you LOGEAN Antoine From chemistry-request@server.ccl.net Thu Feb 28 12:16:57 2002 Received: from gatekeeper.tripos.com (firewall-user@[192.160.145.62]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1SHGv501054 for ; Thu, 28 Feb 2002 12:16:57 -0500 Received: (from uucp@localhost) by tripos.com (8.8.8+Sun) id LAA25240 for ; Thu, 28 Feb 2002 11:16:30 -0600 (CST) Received: from celaeno.tripos.com(172.20.5.232) by gatekeeper.tripos.com via smap (V5.5) id xma025220; Thu, 28 Feb 02 11:15:42 -0600 Received: from oculus.tripos.com ([172.20.5.253]) by celaeno.tripos.com with esmtp (Exim 3.33 #4) id 16gU9a-0006kn-00 for chemistry@ccl.net; Thu, 28 Feb 2002 11:15:38 -0600 Received: from Unknown [172.20.5.232] by oculus.tripos.com - SuperScout Email Filter ; Thursday, 28 February 2002, 11:15:37 Message-ID: <3C7E65B8.688926AD@tripos.com> From: David Larson To: CHEMISTRY@ccl.net Reply-To: bclark@tripos.com Date: Thu, 28 Feb 2002 11:15:36 -0600 Subject: Call for Papers for Fall ACS in Boston MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="--=_NextPart_ST_11_15_37_Thursday_February_28_2002_6249" X-Mailer: Mozilla 4.7C-SGI [en] (X11; U; IRIX 6.5 IP32) X-Accept-Language: en Sender: dlarson@tripos.com Organization: Tripos, Inc. http://www.tripos.com This is a multi-part message in MIME format. ----=_NextPart_ST_11_15_37_Thursday_February_28_2002_6249 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit ********************************************************************* ******** The deadline for abstract submissions is 1 April ********* ********************************************************************* QSAR IN THE BRAVE NEW WORLD OF STRUCTURAL BIOLOGY, GENOMICS, COMBICHEM AND HTS Fall ACS meeting in Boston (August 18-22, 2002) Sponsored by the Division of Computers in Chemistry (COMP) The scope of QSAR includes analysis of all aspects of quantitative molecular design. 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Hanley Road St. Louis MO 63144 Yvonne Martin (yvonne.c.martin@abbott.com) D-47E AP10/2 Abbott Laboratories 100 Abbott Park Road Abbott Park IL 60064-6100 ----=_NextPart_ST_11_15_37_Thursday_February_28_2002_6249 Content-Type: text/x-vcard; charset=us-ascii; name="dlarson.vcf" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="dlarson.vcf" Content-Description: Card for David Larson begin:vcard n:Larson;David A. tel;fax:314-647-9241 tel;work:314-647-8837 x3318 x-mozilla-html:FALSE org:TRIPOS, Inc. adr:;;1699 S. Hanley Road;St. Louis;MO;63144; version:2.1 email;internet:dlarson@tripos.com title:Senior Support Scientist note;quoted-printable:Please Send Requests For Technical=0D=0ASupport to 'support@tripos.com'.=0D=0ASYBYL 6.8/UNITY 4.3/MixCD 1.5 now available. x-mozilla-cpt:;-29824 fn:David Larson end:vcard ----=_NextPart_ST_11_15_37_Thursday_February_28_2002_6249-- From chemistry-request@server.ccl.net Thu Feb 28 13:19:29 2002 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1SIJT502501 for ; Thu, 28 Feb 2002 13:19:29 -0500 Received: from cornell.edu ([128.84.182.122]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id NAA12588; Thu, 28 Feb 2002 13:18:56 -0500 (EST) Sender: richard@cornell.edu Message-ID: <3C7E7490.8AC9F9F9@cornell.edu> Date: Thu, 28 Feb 2002 13:18:56 -0500 From: Richard Gillilan X-Mailer: Mozilla 4.77 [en] (X11; U; Linux 2.4.16 i686) X-Accept-Language: en MIME-Version: 1.0 To: Logean Antoine CC: chemistry@ccl.net Subject: Re: CCL:A little geometrical problem References: <000e01c1c077$1751e9d0$2d554f82@hit4> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Use the formula for rotation of a point about an arbitrary axis. You can find it derived in Goldstein's classical mechanics text (and probably many other books). A google search "rotate a point about an axis" will turn up lots of hits. There is also a matrix version of the algorithm (Computer Graphics Foley and van Dam?) and also a section written by Mike Pique in a volume of Graphics Gems. I believe the formula has an important historical connection to theory of quaternions (Rodrigues rotation formula). Richard Gillilan MacCHESS Cornell Logean Antoine wrote: > > A little geometrical problem : > > Taken a residue in a PDB file, how can I calculate the Cartesian > coordinates of CB when I know the coordinates of N, CA and C, the angle > N-CA-CB, C-CA-CB and the bond length CA-CB ? > > It seems to be trivial but I am unable to find a solution ! > > I am sure that somebody can help me. > > In advance thank you > > LOGEAN Antoine From chemistry-request@server.ccl.net Thu Feb 28 13:54:30 2002 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1SIsU503477 for ; Thu, 28 Feb 2002 13:54:30 -0500 Received: from cornell.edu ([128.84.182.122]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id NAA07187; Thu, 28 Feb 2002 13:54:00 -0500 (EST) Sender: richard@cornell.edu Message-ID: <3C7E7CC8.2BA34856@cornell.edu> Date: Thu, 28 Feb 2002 13:54:00 -0500 From: Richard Gillilan X-Mailer: Mozilla 4.77 [en] (X11; U; Linux 2.4.16 i686) X-Accept-Language: en MIME-Version: 1.0 To: Logean Antoine CC: chemistry@ccl.net Subject: Re: CCL:A little geometrical problem References: <000e01c1c077$1751e9d0$2d554f82@hit4> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Ooops. Sorry Logean, I spoke too soon, although you should be able to use the formula I suggested, it's not as simple as I thought. Here's what I was thinking: Write down the the formula for rotation of CB about the C-CA axis. Do the same for rotation of CB about the CA-N axis. Set them equal. This should give you 3 equations, 3 unknowns. Could be a mess to solve though, Perhaps someone can suggest a clever solution. Richard Logean Antoine wrote: > > A little geometrical problem : > > Taken a residue in a PDB file, how can I calculate the Cartesian > coordinates of CB when I know the coordinates of N, CA and C, the angle > N-CA-CB, C-CA-CB and the bond length CA-CB ? > > It seems to be trivial but I am unable to find a solution ! > From chemistry-request@server.ccl.net Thu Feb 28 13:25:20 2002 Received: from ucidoor.unitedcatalysts.com ([208.23.162.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1SIPJ502739 for ; Thu, 28 Feb 2002 13:25:19 -0500 Received: by ucidoor.unitedcatalysts.com; (8.8.8/1.3/10May95) id NAA30524; Thu, 28 Feb 2002 13:24:45 -0500 (EST) Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Thu, 28 Feb 2002 13:22:09 -0500 (Eastern Standard Time) Received: from lvlxch01.unitedcatalysts.com ([10.16.100.88]) by lvlmail.unitedcatalysts.com (PMDF V6.0-24 #41777) with ESMTP id <0GS9007A59JYCA@lvlmail.unitedcatalysts.com>; Thu, 28 Feb 2002 13:19:10 -0500 (EST) Received: by lvlxch01.unitedcatalysts.com with Internet Mail Service (5.5.2650.21) id ; Thu, 28 Feb 2002 13:22:59 -0500 Content-return: allowed Date: Thu, 28 Feb 2002 13:22:49 -0500 From: "Shobe, Dave" Subject: RE: A little geometrical problem To: "'Logean Antoine'" , "'CCL'" Message-id: <157A51F55AAAD3119CD70008C7B1629D01C159F9@lvlxch01.unitedcatalysts.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g1SIPK502740 I don't have a program to recommend, but if you're building your own here is an idea. The problem is related to converting from spherical to Cartesian coordinates. With CA as the origin and the C-CA bond along the (negative) z axis, we have in terms of *local* Cartesian coordinates (xloc, yloc, zloc): zloc = r * cos(180° - alpha) yloc = r * sin(180° - alpha) cos(beta) xloc = r * sin(180° - alpha) sin(beta) with r, alpha, beta equaling the CA-CB distance, the C-CA-CB bond angle, and the N-C-CA-CB torsion angle. Now that you have (xloc, yloc, zloc) you need to convert them into the coordinates being used for the molecule. This is a Cartesian to Cartesian conversion so it's just a matter of finding the right matrix to multiply the vector by. --David Shobe Süd-Chemie Inc. phone (502) 634-7409 fax (502) 634-7724 email dshobe@sud-chemieinc.com Don't bother flaming me: I'm behind a firewall. -----Original Message----- From: Logean Antoine [mailto:alogean@aspirine.u-strasbg.fr] Sent: Thursday, February 28, 2002 11:44 AM To: chemistry@ccl.net Subject: CCL:A little geometrical problem A little geometrical problem : Taken a residue in a PDB file, how can I calculate the Cartesian coordinates of CB when I know the coordinates of N, CA and C, the angle N-CA-CB, C-CA-CB and the bond length CA-CB ? It seems to be trivial but I am unable to find a solution ! I am sure that somebody can help me. In advance thank you LOGEAN Antoine -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Thu Feb 28 12:59:01 2002 Received: from chem.umn.edu ([128.101.157.2]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g1SHx0502068 for ; Thu, 28 Feb 2002 12:59:00 -0500 Received: (qmail 51706 invoked by uid 1120); 28 Feb 2002 11:58:34 -0600 Received: from localhost (sendmail-bs@127.0.0.1) by localhost with SMTP; 28 Feb 2002 11:58:34 -0600 Date: Thu, 28 Feb 2002 11:58:34 -0600 (CST) From: Lakshmi Devi Kesavan To: Logean Antoine cc: chemistry@ccl.net Subject: Re: CCL:A little geometrical problem In-Reply-To: <000e01c1c077$1751e9d0$2d554f82@hit4> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, If you are using charmm, this can be done using the command 'IC build' (one could refer to the doc file 'ic.doc') and then writing out the cartesian coordinate of the molecule. hope that helps. Devi ************************* Lakshmi S Devi Kesavan Doctoral Candidate Department of Chemistry 207, Pleasant Street S.E, University of Minnesota Minneapolis, MN 55455-0431 Off # : 612-625-2909 ************************* On Thu, 28 Feb 2002, Logean Antoine wrote: > A little geometrical problem : > > Taken a residue in a PDB file, how can I calculate the Cartesian > coordinates of CB when I know the coordinates of N, CA and C, the angle > N-CA-CB, C-CA-CB and the bond length CA-CB ? > > It seems to be trivial but I am unable to find a solution ! > > I am sure that somebody can help me. > > In advance thank you > > LOGEAN Antoine > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Thu Feb 28 16:41:57 2002 Received: from dirf.bris.ac.uk ([137.222.10.72]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1SLfv506068 for ; Thu, 28 Feb 2002 16:41:57 -0500 Received: from fsa.bris.ac.uk by dirf.bris.ac.uk with SMTP-PRIV with ESMTP; Thu, 28 Feb 2002 21:41:14 +0000 Received: (from nobody@localhost) by fsa.bris.ac.uk (8.11.6/8.11.6) id g1SLePO25211; Thu, 28 Feb 2002 21:40:25 GMT X-Authentication-Warning: fsa.bris.ac.uk: nobody set sender to chajm@bristol.ac.uk using -f To: chemistry@ccl.net Subject: MGMS International Conference 2002 - Biomolecular Interactions Date: Thu, 28 Feb 2002 21:40:25 +0000 From: Adrian.Mulholland@bristol.ac.uk Message-ID: <1014932425.3c7ea3c915422@webmail.bris.ac.uk> X-Mailer: SilkyMail v1.1.2 21-September-2001 MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Originating-IP: 62.30.104.130 Early Registration and Abstract Submission Deadline Biomolecular Interactions A Conference dedicated to Prof. Peter A. Kollman http://www.chm.bris.ac.uk/enzyme/mgms/outline.html Molecular Graphics and Modelling Society Annual International Conference in conjunction with the British Biophysical Society Wills Hall, University of Bristol, 3-5 April 2002 Early Registrations must be received by Monday March 4th. After this deadline, the registration fee will increase by 50 GBP. The final deadline for registration is Tuesday March 19th. Abstracts for oral or poster presentation should also be submitted by March 4th. Biomolecular Interactions - This conference will bring together leading experts in modelling, theoretical, informatics and experimental approaches to the study of biomolecular interactions, from both academia and industry. The interactions of small ligands with biological macromolecules will be a particular focus. The conference will be dedicated to Prof. Peter A. Kollman, in recognition of his work in the field, and his support of MGMS conferences. The MGMS particularly wishes to encourage the participation of younger researchers. A limited number of bursaries will be available, supported by Chemical Computing Group. The deadline for submission of abstracts is March 4th 2002. See the conference web pages for confirmed speakers and other details: http://www.chm.bris.ac.uk/enzyme/mgms/outline.html --------------------------------------- bio-int@bris.ac.uk ----------------------------------------------------- This mail sent through SilkyMail v1.1.2 From chemistry-request@server.ccl.net Thu Feb 28 18:08:25 2002 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1SN8P508566 for ; Thu, 28 Feb 2002 18:08:25 -0500 Received: from TheWorld.com (pcls1.std.com [199.172.62.103]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id SAA24634 for ; Thu, 28 Feb 2002 18:08:24 -0500 (EST) Received: from vaio.theworld.com (1Cust213.tnt4.bos10.da.uu.net [63.10.168.213]) by TheWorld.com (8.9.3/8.9.3) with ESMTP id SAA27074 for ; Thu, 28 Feb 2002 18:07:57 -0500 Message-Id: <5.1.0.14.1.20020228181403.00a36270@pop.theworld.com> X-Sender: jle@pop.theworld.com X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Thu, 28 Feb 2002 18:16:52 -0500 To: chemistry@ccl.net From: Joe Leonard Subject: MMFF94/docking and initial guesses Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Folks, Searching the CCL archives revealed that the only group which did docking studies with MMFF94 was CTC back in 97-98. Granted, this was a quick search, so I might have missed something - have there been other efforts which show whether this is a good (or bad) FF for such calculations (flexible ligand, etc)? Another question for MMFF94 - I recall people indicating that it's useful when making initial-guess geometries for QM calculations. This makes sense to me given its parameterization, but I was unable (again quickly) to find any examples of this... Anybody have any? Thanks in advance! Joe P.S. Yeah, my email's mutating from jle@world.std.com to jle@theworld.com, so please update your records if you've had it... From chemistry-request@server.ccl.net Thu Feb 28 18:22:16 2002 Received: from schrodinger.com ([192.156.98.99]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1SNMF509020 for ; Thu, 28 Feb 2002 18:22:15 -0500 Received: from schrodinger.com (amaris.schrodinger.com [192.156.98.121]) by schrodinger.com (8.8.5/8.8.5) with ESMTP id PAA06012; Thu, 28 Feb 2002 15:21:17 -0800 Message-ID: <3C7EBD1D.AED96195@schrodinger.com> Date: Thu, 28 Feb 2002 15:28:30 -0800 From: George Vacek Organization: Schrodinger, Inc. X-Mailer: Mozilla 4.75 [en] (Windows NT 5.0; U) X-Accept-Language: en MIME-Version: 1.0 To: Martijn Zwijnenburg CC: chemistry@ccl.net Subject: Re: CCL:experience with semi-empirical MD References: <3C7E48F2.14442.60AED57@localhost> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Martijn Zwijnenburg wrote: > Several people told me, in a reply to my question, that it's possible > to do semi-empirical molecular dynamics (AM1, PM3) with > Hyperchem, Mopac and Spartan. Now I wonder if somebody can > give me some practical information on systems one can treat on a > state of the art linux or windows 2000 machine. Martijn, Mopac 2002 uses the linear scaling MOZYME algorithm, so it can tackle fairly large systems (up to 20000 atom limit) in a reasonable amount of time. For practical purposes, in a dynamics run, after the first time step, additional time steps can be calculated in only a fraction of the time (probably about 1/10th). So for a couple hundred atoms and a time period of, say, 500 femtoseconds, you are probably looking at only a few hours on a decent linux box. I hope that helps. For more information on Mopac 2002, please see http://www.schrodinger.com Schrodinger distributes Mopac 2002 only in North and South America, but the page also lists distributor information for Europe and other regionds if you decide you are interested. Regards, George Vacek =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- vacek@schrodinger.com (503) 299-1150 http://www.schrodinger.com/ Schrodinger, Inc., 1500 SW First Ave., Suite 1180, Portland, OR 97201 Every culture that has lost myth has lost, by the same token, its natural, healthy creativity. -- Friedrich Nietzsche "The Birth of Tragedy" 1872 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- From chemistry-request@server.ccl.net Thu Feb 28 18:48:32 2002 Received: from oc30.uni-paderborn.de ([131.234.240.90]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1SNmV509879 for ; Thu, 28 Feb 2002 18:48:31 -0500 Received: (from ib@localhost) by oc30.uni-paderborn.de (SGI-8.9.3/8.9.3) id DAA15091; Fri, 1 Mar 2002 03:06:07 +0100 (CET) Date: Fri, 1 Mar 2002 03:06:07 +0100 (CET) Message-Id: <200203010206.DAA15091@oc30.uni-paderborn.de> X-Authentication-Warning: oc30.uni-paderborn.de: ib set sender to ib@oc30.uni-paderborn.de using -f From: Ingo Brunberg To: alogean@aspirine.u-strasbg.fr CC: chemistry@ccl.net In-reply-to: <000e01c1c077$1751e9d0$2d554f82@hit4> (alogean@aspirine.u-strasbg.fr) Subject: Re: CCL:A little geometrical problem References: <000e01c1c077$1751e9d0$2d554f82@hit4> Obviously this problem is not as trivial as it seems. Though I can think of a rather complicated solution, I just want to point out, that there is most likely no single solution. The point you are searching is located on the intersection of two cones with the angles N-CA-CB and C-CA-CB originating from CA. So there are three different cases: 1) N-CA-CB + C-CA-CB < N-CA-C: no solution 2) N-CA-CB + C-CA-CB = N-CA-C: one solution 3) N-CA-CB + C-CA-CB > N-CA-C: two solutions Seems like the problem leads to a quadratic equation. Regards, Ingo > A little geometrical problem : > > Taken a residue in a PDB file, how can I calculate the Cartesian > coordinates of CB when I know the coordinates of N, CA and C, the angle > N-CA-CB, C-CA-CB and the bond length CA-CB ? > > It seems to be trivial but I am unable to find a solution ! > > I am sure that somebody can help me. > > In advance thank you > > LOGEAN Antoine From chemistry-request@server.ccl.net Thu Feb 28 19:51:50 2002 Received: from mole.chem.iupui.edu ([134.68.136.192]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g210po512210 for ; Thu, 28 Feb 2002 19:51:50 -0500 Received: from mole.chem.iupui.edu (mole.chem.iupui.edu [134.68.136.192]) by mole.chem.iupui.edu (8.9.1/8.9.1) with ESMTP id TAA318416; Thu, 28 Feb 2002 19:49:46 -0500 (EST) Date: Thu, 28 Feb 2002 19:49:45 -0500 From: Daquan Gao To: Ingo Brunberg cc: alogean@aspirine.u-strasbg.fr, chemistry@ccl.net Subject: Re: CCL:A little geometrical problem In-Reply-To: <200203010206.DAA15091@oc30.uni-paderborn.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII That is about right. The condition No. 2) leads to inifinitely many solutions.... The points of possible CB forms a circle. By the way, the only anlges that satifsy this condition are: N-CA-C=180 ! Daquan On Fri, 1 Mar 2002, Ingo Brunberg wrote: > Obviously this problem is not as trivial as it seems. Though I can > think of a rather complicated solution, I just want to point out, that > there is most likely no single solution. The point you are searching > is located on the intersection of two cones with the angles N-CA-CB > and C-CA-CB originating from CA. So there are three different cases: > > 1) N-CA-CB + C-CA-CB < N-CA-C: no solution > 2) N-CA-CB + C-CA-CB = N-CA-C: one solution > 3) N-CA-CB + C-CA-CB > N-CA-C: two solutions > > Seems like the problem leads to a quadratic equation. > > Regards, > > Ingo > > > A little geometrical problem : > > > > Taken a residue in a PDB file, how can I calculate the Cartesian > > coordinates of CB when I know the coordinates of N, CA and C, the angle > > N-CA-CB, C-CA-CB and the bond length CA-CB ? > > > > It seems to be trivial but I am unable to find a solution ! > > > > I am sure that somebody can help me. > > > > In advance thank you > > > > LOGEAN Antoine > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > From chemistry-request@server.ccl.net Thu Feb 28 20:48:54 2002 Received: from mole.chem.iupui.edu ([134.68.136.192]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g211ms513798 for ; Thu, 28 Feb 2002 20:48:54 -0500 Received: from mole.chem.iupui.edu (mole.chem.iupui.edu [134.68.136.192]) by mole.chem.iupui.edu (8.9.1/8.9.1) with ESMTP id UAA317267; Thu, 28 Feb 2002 20:46:59 -0500 (EST) Date: Thu, 28 Feb 2002 20:46:59 -0500 From: Daquan Gao To: Ingo Brunberg cc: alogean@aspirine.u-strasbg.fr, chemistry@ccl.net Subject: Re: CCL:A little geometrical problem In-Reply-To: <200203010206.DAA15091@oc30.uni-paderborn.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I thought about this again, found my previous answer was not complete. Condition 2) can be satified when N-CA-C <= 180. If N-CA-C = 180, there are infinitely many solutions; when N-CA-C<180 and equals the sum of the other two angles, one solution. Regards, daquan On Fri, 1 Mar 2002, Ingo Brunberg wrote: > Obviously this problem is not as trivial as it seems. Though I can > think of a rather complicated solution, I just want to point out, that > there is most likely no single solution. The point you are searching > is located on the intersection of two cones with the angles N-CA-CB > and C-CA-CB originating from CA. So there are three different cases: > > 1) N-CA-CB + C-CA-CB < N-CA-C: no solution > 2) N-CA-CB + C-CA-CB = N-CA-C: one solution > 3) N-CA-CB + C-CA-CB > N-CA-C: two solutions > > Seems like the problem leads to a quadratic equation. > > Regards, > > Ingo > > > A little geometrical problem : > > > > Taken a residue in a PDB file, how can I calculate the Cartesian > > coordinates of CB when I know the coordinates of N, CA and C, the angle > > N-CA-CB, C-CA-CB and the bond length CA-CB ? > > > > It seems to be trivial but I am unable to find a solution ! > > > > I am sure that somebody can help me. > > > > In advance thank you > > > > LOGEAN Antoine > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > >