Dr. Eric = Scerri

Department of Chemistry & = Biochemistry,

Charles Young Drive,

Los = Angeles,

CA 90095.

310 206 7443

fax: = 310 206 2061

UCLA faculty web page:=A0=A0=A0=

Editor of = Foundations of Chemistry,

International Society for = the Philosophy of Chemistry,

http://ispc.sas.upenn.edu/

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name="dot_trans.gif" Content-Disposition: inline; filename=dot_trans.gif R0lGODlhAQABAID/AMDAwAAAACH5BAEAAAAALAAAAAABAAEAAAICRAEAOw== --Apple-Mail-16-523122418 Content-Transfer-Encoding: base64 Content-Id: <0F39BB0B-6B09-4FC2-9DBD-1C2329F4C24F~!~chem.ucla.edu> Content-Type: image/gif; x-unix-mode=0666; name="dot_trans.gif" Content-Disposition: inline; filename=dot_trans.gif R0lGODlhAQABAID/AMDAwAAAACH5BAEAAAAALAAAAAABAAEAAAICRAEAOw== --Apple-Mail-16-523122418 Content-Transfer-Encoding: base64 Content-Id: <955B49A5-6629-4777-870B-547402BEACA6~!~chem.ucla.edu> Content-Type: image/gif; x-unix-mode=0666; name="dot_trans.gif" Content-Disposition: inline; filename=dot_trans.gif R0lGODlhAQABAID/AMDAwAAAACH5BAEAAAAALAAAAAABAAEAAAICRAEAOw== --Apple-Mail-16-523122418 Content-Transfer-Encoding: base64 Content-Id: Content-Type: image/gif; x-unix-mode=0666; name="dot_trans.gif" Content-Disposition: inline; filename=dot_trans.gif R0lGODlhAQABAID/AMDAwAAAACH5BAEAAAAALAAAAAABAAEAAAICRAEAOw== --Apple-Mail-16-523122418 Content-Transfer-Encoding: base64 Content-Id: <02D83C4A-8887-4BB3-BC32-A7C86F449393~!~chem.ucla.edu> Content-Type: image/gif; x-unix-mode=0666; name="dot_trans.gif" Content-Disposition: inline; filename=dot_trans.gif R0lGODlhAQABAID/AMDAwAAAACH5BAEAAAAALAAAAAABAAEAAAICRAEAOw== --Apple-Mail-16-523122418 Content-Transfer-Encoding: base64 Content-Id: <16DFC400-D963-426A-A392-526B4A2B0B0C~!~chem.ucla.edu> Content-Type: image/gif; x-unix-mode=0666; name="dot_trans.gif" Content-Disposition: inline; filename=dot_trans.gif R0lGODlhAQABAID/AMDAwAAAACH5BAEAAAAALAAAAAABAAEAAAICRAEAOw== --Apple-Mail-16-523122418-- --Apple-Mail-15-523122418-- From owner-chemistry@ccl.net Tue Feb 14 02:53:07 2006 From: "Rajan Vatassery r-vatassery%a%northwestern.edu" To: CCL Subject: CCL: tinker/mm3pro parameter set Message-Id: <-30885-060214012042-20628-j9VzQDQ0EKdLnWp51kBV4w---server.ccl.net> X-Original-From: "Rajan Vatassery" Sent to CCL by: "Rajan Vatassery" [r-vatassery]*[northwestern.edu] Dear CCLers, i've been working on the mm3 parameter set through Tinker (from the Ponder lab) and it's been going great. i tried, however, to make a small jump into mm3pro, the protein-related parameter set, and i've had mixed results. it seems that there are a significant number of atoms that are missing parameterizations in this set. i'm not sure if it's a case of me mis-assigning atom types or if they're just plain missing. so my question is two-fold: A ) i have a ALA-ALA-GLU tripeptide and i disagreed with some of the atom types that PDBXYZ gave so i changed: - any backbone carbonyl oxygens from 14 (Carboxylate) to 13 (Amide). the only O-14 is on the r group of the GLU. - any backbone carbonyl carbons from 3 (carboxyl) to 2 (amide) is this the correct parameterization? B ) most of the missing parameters are ones that, in my opinion, should be included (for example, the 3-13 stretch). this makes me think that i'm somehow miscategorizing the atoms. if this isn't the case, then can i simply port the missing parameters from the regular mm3 file or are the two sets incompatible? my other option is converting to mm3, but that would be quite a hassle. web searches turn up nothing, nor does the CCL archive. this is the error i get from tinker when i use these parameters: ************** start ********************************* Undefined Bond Stretching Parameters : Type Atom Names Atom Classes Bond 34-C 35-O 3 13 Undefined Angle Bending Parameters : Type Atom Names Atom Classes Angle 29-C 30-C 38-C 1 2 1 Angle 33-C 34-C 35-O 1 3 13 Angle 35-O 34-C 36-O- 13 3 14 Undefined Out-of-Plane Bending Parameters : Type Atom Names Atom Classes Angle-OP 34-C 35-O 3 13 Undefined Torsional Parameters : Type Atom Names Atom Classes Torsion 28-N 29-C 30-C 38-C 8 1 2 1 Torsion 32-C 29-C 30-C 38-C 1 1 2 1 Torsion 39-H 29-C 30-C 38-C 17 1 2 1 Torsion 29-C 30-C 38-C 37-H 1 2 1 17 Torsion 29-C 30-C 38-C 44-H 1 2 1 17 Torsion 29-C 30-C 38-C 45-H 1 2 1 17 Torsion 32-C 33-C 34-C 35-O 1 1 3 13 Torsion 42-H 33-C 34-C 35-O 17 1 3 13 Torsion 43-H 33-C 34-C 35-O 17 1 3 13 MECHANIC -- Some Required Potential Energy Parameters are Undefined TINKER is Unable to Continue; Terminating the Current Calculation *********************************** end **************************** thanks in advance for your help raj r-vatassery+^+northwestern.edu http://pubweb.northwestern.edu/~rnv470 From owner-chemistry@ccl.net Tue Feb 14 03:28:00 2006 From: "Marc Baaden baaden{=}smplinux.de" To: CCL Subject: CCL: Lanthanide parameters Message-Id: <-30886-060214030357-23851-kMUeJTATMFGYKBOaS3tqLA-*-server.ccl.net> X-Original-From: Marc Baaden Content-Type: text/plain; charset=us-ascii Date: Tue, 14 Feb 2006 09:03:41 +0100 Mime-Version: 1.0 Sent to CCL by: Marc Baaden [baaden]_[smplinux.de] Hi, I don't quite know whether you are looking for gas phase salt-like compounds only or also for solution data. We have looked at La3+, Eu3+ and Yb3+ in acetonitrile solution as well as triflate and perchlorate salts. Both QM and MM methods were used to look at structural features. [1] Marc Baaden [1] M. Baaden, F. Berny, G. Wipff and C. Madic A molecular dynamics and quantum mechanics study of M3+ lanthanide catio solvation by acetonitrile: the role of cation size, counterions and polarization effects investigated. J. Phys. Chem. A, 104, 2000, 7659-7671. >>> "CCL CCL computationalchemist(_)gmail.com" said: >> Dear CCLers, >> Could anyone help me by giving the some of the lanthanide compounds >> molecular strucuture and the parameters like bond length, bond angle for >> various lanthanide and actinide compounds like laf3,la203,las,ceo2,ce203, >> etc. >> Any pointers or papers will be greatly helpful. >> regards, >> sanjay Marc Baaden -- Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris mailto:baaden%a%smplinux.de - http://www.baaden.ibpc.fr FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217 From owner-chemistry@ccl.net Tue Feb 14 04:02:04 2006 From: "Marc Baaden baaden,smplinux.de" To: CCL Subject: CCL: suggestions for manual docking and building Message-Id: <-30887-060214031831-2583-+lF2LP0yYsqgWnez8hTc8Q.@.server.ccl.net> X-Original-From: Marc Baaden Content-Type: text/plain; charset=us-ascii Date: Tue, 14 Feb 2006 09:18:22 +0100 Mime-Version: 1.0 Sent to CCL by: Marc Baaden [baaden^_^smplinux.de] Hi, sorry for the late reply.. In addition to the solutions already mentioned you could also use the following approaches: VMD with NAMD using the AutoIMD plugin or just plain IMD. Requires a starting structure and parameters for it (there are readily available parameter files for the most common compounds, eg proteins, DNA, some lipids). From this point its quite intuitive. If you have virtual reality gear (eg a Spaceball, haptic devices like a Phantom) that adds to it, but keyboard/mouse is of course possible. I think this solution satisfies all your criteria. Get some details eg here [1]. Another tool with similar capacities, but in a more integrated and polished packaging would be Yasara [2]. It has several versions, one is free. But for the docking/building manipulations you would need a non-free (but still affordable) version. Yasara also has built-in capacities for automatic parameterization of unknown compounds. It satisfies your criteria, too. We have successfully used it in the past to manually and interactively dock a peptide into an enzyme active site, whereas automatic docking did not yield such hits. [3] Marc [1] http://www.ks.uiuc.edu/Research/vmd/plugins/autoimd/ [2] http://www.yasara.org/ [3] M. Baaden M and M. S. P. Sansom OMPT: Molecular Dynamics simulations of an outer membrane enzyme. Biophys. J., 87, 2004, 2942-2953 >>> "Bruce Palfey brupalf|*|umich.edu" said: >> Sent to CCL by: Bruce Palfey [brupalf^-^umich.edu] >> Hi >> >> I was wondering if people could suggest a good program for manually >> and interactively building protein-ligand or nucleic acid-ligand >> complexes. Characteristics of the ideal program are: >> >> - Direct. I'd like to be able to grab one molecule and maneuver it >> into a position I think is interesting using simple, direct mouse and/ >> or keyboard controls. >> >> - Easily loaded. The molecules - either macro or micro - would most >> likely come from different pdb files, though support of other formats >> would also be helpful. A minimum of file preparation/conversion is >> desirable. >> >> - Intuitive. The students who pass through my lab should be able to >> just pick it up and go; we need a tool to support our research, >> rather than a system to dedicate our efforts to mastering. >> >> - Available for common cheap platforms. I'd like to use this on PC's >> in my lab or on my Mac laptop, or both. >> >> - Supports hardware stereo. It seems to me that that's the best way >> to build. >> >> - Free. Or cheap. Or at least a good value worthy of an investment. >> >> I welcome all suggestions, and will summarize what I learn. >> >> ciao, >> Bruce Palfey >> Department of Biological Chemistry >> University of Michigan Medical School >> Ann Arbor, MI 48109-0606>> >> >> Marc Baaden -- Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris mailto:baaden{:}smplinux.de - http://www.baaden.ibpc.fr FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217 From owner-chemistry@ccl.net Tue Feb 14 05:21:00 2006 From: "jan Labanowski janl _ speakeasy.net" To: CCL Subject: CCL: Small changes in CCL mail distribution -- please read. Message-Id: <-30888-060214051132-15732-RZfS+yqzoSRBmiJ9sYbjVQ]^[server.ccl.net> X-Original-From: "jan Labanowski" Date: Tue, 14 Feb 2006 05:11:27 -0500 Sent to CCL by: "jan Labanowski" [janl]-[speakeasy.net] Dear CCL Subscribers... Since I am getting occasionally e-mails "stop my CCL message", let me explain that I usually cannot. Once the mail starts distributing the messages, it is too late, since the thing takes often only seconds. As you all know, to prevent spammers from sending stuff to CCL > from faked/borrowed addresses, the mail had to be confirmed by you, or I had to give it a passing glance and release it. If it comes from someone I know/remember, I release it without reading it. But it is not good... To err is human, and you sometime forget that when you respond to the CCL message your mail ALWAYS GOES TO CCL. There is no such thing as responding to the author of the message on CCL. If you want to respond to the author, you have to MANUALLY TYPE his/her address on the To: line of your message (more later, if you care...). This prompted me to make a small procedural change. From now on, I will not release email to CCL if it is not confirmed by you. I added a few things to my Web interface that will help me doing this. and hopefully did not mess up other things and will work great. I still have to release e-mail manually in the case when you are posting for the first time from some email address, or when the scripts stopped email because there is something fishy about it (e.g., it contains an attachment, or there is no chemistry]=[ccl.net on the To: or Cc: line, and zillions other things). I also decided to make your life easier a bit when you use the mail sending form available from the CCL Home page: http://server.ccl.net/cgi-bin/ccl/send_ccl_message Now, it will only ask for confirmation if you are sending mail to CCL Subscribers -- the mail to Administrator will be sent right away. It seems that retyping the number depicted by the GIF image works well (though still a few jerks tries a few times a day). When you respond to CCL message, your mail GOES TO CCL Subscribers. It will NEVER go automatically to the author of the message. NEVER!!! In MOST cases it will go to CCL subscribers. In few cases, when you do not have a standard setup, it will go to TRASH box of CCL together with bounces, viruses, and spam. If you want to replay to the AUTHOR but NOT TO CCL, you have to MANUALLY retype the author address in the To: field, i.e., erase what is there, and type in the real mail of the person. There is NO OTHER WAY. The original author's email address is always messed up/obfuscated by CCL distribution software. How to recover the real author's address is in: http://server.ccl.net/chemistry/aboutccl/instructions/index.shtml The From address on the message that you received from CCL is no longer an email address of the author. The author email address is messed up intentionally, so the virus and spam does not hurt the people who post to CCL. What is really on the From: line is the modified author address with the "]=[" sign replaced with some garbage given as a comment and often mixed up with the author's name. The real email address on the from line (the one that computer understand) is . The rest are "comments". You already know that if you send something to it goes to TRASH without reading. But from comments on the From: line of the message you can easily guess what is the real address. For example: From: "Joe Shmoe joe %% shmoepc.com" The author's address is joe]=[shmoepc.com, but no software will do it for you. You have to type it yourself in the To: field of the message that you are sending. Otherwise it will go to all of us or to TRASH and we will have fun occasionally. Now, since I am no longer resending your messages without confirmation, it will be harder to blame me. Note, that you have a DELETE option when you are asked for confirmation. By all means USE IT when you do not want the message to go to the whole CCL list. If your confirmation request is stuck and you did not get within minutes from posting to CCL, please let me know, and I will look at it. Thank you for your cooperation... Jan Labanowski CCL Admin jkl]=[ccl.net From owner-chemistry@ccl.net Tue Feb 14 06:19:03 2006 From: "XunLei Ding dxl a ustc.edu.cn" To: CCL Subject: CCL:G: Lowdin and Mulliken population Message-Id: <-30889-060214045029-5299-WbEX8TpzIVGdIn2kX85gqQ%a%server.ccl.net> X-Original-From: "XunLei Ding" Content-Type: text/plain Date: Tue, 14 Feb 2006 17:07:17 +0800 Sent to CCL by: "XunLei Ding" [dxl+*+ustc.edu.cn] Dear Sir, Data using 6-311+G(3df) and cc-pvtz are list below. It is true, as you told me, that Mulliken depend much on the basis sets. But the biggest question is: Lowdin always give the opposite values. I don't think it is due to basis depending. Thank you very much! Yours, Ding cc-pvtz NBO Mulliken Lowdin C charge 0.91 0.31 -0.54 O charge -0.45 -0.15 0.27 6311 NBO Mulliken Lowdin C charge 0.96 1.01 -0.47 O charge -0.47 -0.50 0.23 In your mail: >From: "S.I.Gorelsky gorelsky[]stanford.edu" >Reply-To: "CCL Subscribers" >To: "Xunlei, Ding " >Subject: CCL:G: Lowdin and Mulliken population >Date:Sun, 12 Feb 2006 22:38:13 -0500 > >Sent to CCL by: "S.I.Gorelsky" [gorelsky|-|stanford.edu] > > This is hardly surprising: you are using the 6-311+G(3df) basis set and > MPA charges(populations) derived from calculations with diffuse(+) > functions are bound to fail. For more details, you can check the AOMix > manual, pages 7 and 57 (http://www.sg-chem.net/aomix). > > My recommendation: try to run your calculation with the TZVP basis set. > Then both MPA and LPA should give you the reasonable numbers. > > Regards, > > S.G. > > On Sun, 12 Feb 2006, Ding Xunlei ding . sissa.it wrote: > > > Sent to CCL by: Ding Xunlei [ding#sissa.it] > > Dear All, > > > > Using Gaussian03 with the input file below, we can get the Mulliken and > > Lowdin charge populations on CO2 molecule. But the results are totally > > opposite, as: > > > > Mulliken atomic charges: > > 1 C 1.006159 (lose electrons) > > 2 O -0.503080 > > 3 O -0.503080 > > Lowdin Atomic Charges: > > 1 C -0.465607 (get electrons?) > > 2 O 0.232804 > > 3 O 0.232804 > > > > Why? > > Thank you! > > > > Yours, > > Ding > > > > #pbepbe/6-311+G(3df) opt iop(6/80=1) > > > > mp2 > > > > 0 1 > > C > > O 1 1.16 > > O 1 1.16 2 180.0> > > > > > > ---------------------------------------------------------------- > Dr S.I. Gorelsky, Department of Chemistry, Stanford University > Box 155, 333 Campus Drive, Stanford, CA 94305-5080 USA > Phone: (650) 723-0041. Fax: (650) 723-0852. > ----------------------------------------------------------------> > > > From owner-chemistry@ccl.net Tue Feb 14 09:51:00 2006 From: "Sebastian Rohrer sebastian.rohrer+/-mail.uni-wuerzburg.de" To: CCL Subject: CCL: Multiple Docking Poses in OpenEye Fred Message-Id: <-30890-060214082108-25064-XaFf6Z8WQoRk3hqJkLYt4w ~~ server.ccl.net> X-Original-From: Sebastian Rohrer Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 14 Feb 2006 13:14:32 +0100 MIME-Version: 1.0 Sent to CCL by: Sebastian Rohrer [sebastian.rohrer]|[mail.uni-wuerzburg.de] Hi all, does anybody know how I can get OpenEye's FRED to enumerate multiple docking solutions (poses) per molecule in the output? FlexX does this, but I really would prefer using FRED... I read the manual up and down, but somehow I am too blind (or too stupid) to find the right option... Thanks a lot, Sebastian -- Sebastian Rohrer AK Baumann - Molecular Modelling Group Department of Pharmaceutical Chemistry Institute of Pharmacy and Food Chemistry University of Wuerzburg Am Hubland 97074 Wuerzburg Germany From owner-chemistry@ccl.net Tue Feb 14 10:55:00 2006 From: "Paul Hawkins phawkins.:.eyesopen.com" To: CCL Subject: CCL: Multiple Docking Poses in OpenEye Fred Message-Id: <-30891-060214105327-13142-MnlCbBV028zsJo19gypwMA===server.ccl.net> X-Original-From: Paul Hawkins Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 14 Feb 2006 08:50:43 -0700 MIME-Version: 1.0 Sent to CCL by: Paul Hawkins [phawkins*eyesopen.com] Sebastien, If you are using a version of FRED after 2.0 there is a num_alt_poses option. In FRED 2.0 this parameter has a maximum of 9, in later versions the maximum is 99. If you have an older version of FRED you may request an evaluation of a the newest release at www.eyesopen.com The eval request link is on the right hand side of the page. Paul. Paul Hawkins Senior Applications Scientist OpenEye Scientific Software Sebastian Rohrer sebastian.rohrer+/-mail.uni-wuerzburg.de wrote: >Sent to CCL by: Sebastian Rohrer [sebastian.rohrer]|[mail.uni-wuerzburg.de] >Hi all, > >does anybody know how I can get OpenEye's FRED to enumerate multiple >docking solutions (poses) per molecule in the output? FlexX does this, >but I really would prefer using FRED... I read the manual up and down, >but somehow I am too blind (or too stupid) to find the right option... > >Thanks a lot, > >Sebastian > > > From owner-chemistry@ccl.net Tue Feb 14 11:30:00 2006 From: "Jim Kress ccl_nospam],[kressworks.com" To: CCL Subject: CCL: tinker/mm3pro parameter set Message-Id: <-30892-060214111728-1653-978xi8FSaI200BdKaGjEKQ-#-server.ccl.net> X-Original-From: "Jim Kress" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 14 Feb 2006 11:17:12 -0500 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam(!)kressworks.com] Jay Ponder et al make it very clear, in the users manual if you read it, that: a) not all parameters from a given force field may exist (esp mm3pro) b) if you make any changes to any parameter files you do so at your own risk So, the error you see are due to your changes in the mm3pro parameter file. If you want to get rid of the errors you will have to recreate all combinations of all the entries in the mm3pro parameter file that are affected by your changes. This includes bond stretch, bond angle, dihedrals, VdW, charges, etc. Jim > -----Original Message----- > From: Rajan Vatassery r-vatassery%a%northwestern.edu > [mailto:owner-chemistry++ccl.net] > Sent: Tuesday, February 14, 2006 3:19 AM > To: Kress, Jim > Subject: CCL: tinker/mm3pro parameter set > > Sent to CCL by: "Rajan Vatassery" > [r-vatassery]*[northwestern.edu] Dear CCLers, i've been > working on the mm3 parameter set through Tinker (from the > Ponder lab) and it's been going great. i tried, however, to > make a small jump into mm3pro, the protein-related parameter > set, and i've had mixed results. it seems that there are a > significant number of atoms that are missing > parameterizations in this set. i'm not sure if it's a case of > me mis-assigning atom types or if they're just plain missing. > so my question is two-fold: > > A ) > > i have a ALA-ALA-GLU tripeptide and i disagreed with some of > the atom types that PDBXYZ gave so i changed: > > - any backbone carbonyl oxygens from 14 (Carboxylate) to 13 > (Amide). the only O-14 is on the r group of the GLU. > > - any backbone carbonyl carbons from 3 (carboxyl) to 2 (amide) > > is this the correct parameterization? > > B ) > > most of the missing parameters are ones that, in my opinion, > should be included (for example, the 3-13 stretch). this > makes me think that i'm somehow miscategorizing the atoms. if > this isn't the case, then can i simply port the missing > parameters from the regular mm3 file or are the two sets > incompatible? my other option is converting to mm3, but that > would be quite a hassle. web searches turn up nothing, nor > does the CCL archive. > > this is the error i get from tinker when i use these parameters: > > ************** start ********************************* > > > Undefined Bond Stretching Parameters : > > Type Atom Names Atom Classes > > Bond 34-C 35-O 3 13 > > Undefined Angle Bending Parameters : > > Type Atom Names Atom Classes > > Angle 29-C 30-C 38-C 1 2 1 > Angle 33-C 34-C 35-O 1 3 13 > Angle 35-O 34-C 36-O- 13 3 14 > > Undefined Out-of-Plane Bending Parameters : > > Type Atom Names Atom Classes > > Angle-OP 34-C 35-O 3 13 > > Undefined Torsional Parameters : > > Type Atom Names > Atom Classes > > Torsion 28-N 29-C 30-C 38-C > 8 1 2 1 > Torsion 32-C 29-C 30-C 38-C > 1 1 2 1 > Torsion 39-H 29-C 30-C 38-C > 17 1 2 1 > Torsion 29-C 30-C 38-C 37-H > 1 2 1 17 > Torsion 29-C 30-C 38-C 44-H > 1 2 1 17 > Torsion 29-C 30-C 38-C 45-H > 1 2 1 17 > Torsion 32-C 33-C 34-C 35-O > 1 1 3 13 > Torsion 42-H 33-C 34-C 35-O > 17 1 3 13 > Torsion 43-H 33-C 34-C 35-O > 17 1 3 13 > > MECHANIC -- Some Required Potential Energy Parameters are Undefined > > TINKER is Unable to Continue; Terminating the Current Calculation > > *********************************** end **************************** > > > > thanks in advance for your help > > raj > > r-vatassery+^+northwestern.edu > http://pubweb.northwestern.edu/~rnv470 > > > > -= This is automatically added to each message by the mailing > script =- To recover the email address of the author of the > message, please change the strange characters on the top line > to the ++ sign. You can also look up the X-Original-From: line > in the mail header.> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, > Password: search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+ > > > > > > From owner-chemistry@ccl.net Tue Feb 14 12:05:01 2006 From: "Bienstock, Rachelle \(NIH/NIEHS\) C biensto1/a\niehs.nih.gov" To: CCL Subject: CCL: CHARMM, RDOCK and Amidation Message-Id: <-30893-060214115600-32657-HXerKBiV3iM/d7r9fmxGPg::server.ccl.net> X-Original-From: "Bienstock, Rachelle \(NIH/NIEHS\) [C]" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 14 Feb 2006 11:08:50 -0500 MIME-Version: 1.0 Sent to CCL by: "Bienstock, Rachelle \(NIH/NIEHS\) [C]" [biensto1||niehs.nih.gov] Hi Folks: I am trying to dock some amidated peptides with a protein and am using the ZDOCK/RDOCK programs. However it appears that RDOCk (CHARMM) is not parameterized to recognize the terminal amide group designated AMDE. Does anyone have experience with this or creating an RTF file for a group who can guide me on the steps I need to take to include a new group which would be recognized by CHARMM and RDOCK? Thanks, Rachelle Dr. Rachelle J. Bienstock Molecular Modeling and Structural Biochemistry National Institutes of Health (NIH) National Institute of Environmental Health Sciences (NIEHS) ITSS P.O. Box 12233 MD F0-011 Research Triangle Park, NC 27709, USA Tel: (919) 541-3397 Fax: (919) 541-5737 Website: http://dir.niehs.nih.gov/dirmmcf/ From owner-chemistry@ccl.net Tue Feb 14 12:40:00 2006 From: "Sengen Sun sengensun++yahoo.com" To: CCL Subject: CCL:G: Lowdin and Mulliken population Message-Id: <-30894-060214120013-2368-Ph8lMWaIPUMF4XZgN1PYMA::server.ccl.net> X-Original-From: Sengen Sun Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Tue, 14 Feb 2006 09:00:08 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Sengen Sun [sengensun!=!yahoo.com] In my experience, I did not see any significant differences (conceptually) between Mulliken and Natural charges as soon as I avoid a diffuse function basis set. I use and like both of them. Both of them always gave me the same conceptual conclusions. However, if it is a common view that Natural charges are more reliable than Mulliken charges, I will have to use NPA from now on. But this does not change my mechanistic conclusions I made before. Maybe I am wrong, but even on a diffuse function basis set, Mulliken charges do NOT ALWAYS fail. They only fail more frequently. It is a little over stating that "you are using the 6-311+G(3df) basis set and MPA charges(populations) derived from calculations with diffuse(+) functions are bound to fail." The numbers in Ding Xunlei's example clearly indicates to me that the Mulliken charges are qualitatively reasonable with a diffuse function basis set in this particular case, while Lowdin Atomic Charges are absurd. I am not that bothered by being "too ionic". Am I confused? Sengen > -------------------------------------------------------------------------------- > > Sent to CCL by: Jens Spanget-Larsen > [spanget#,#ruc.dk] > Dear Ding, > > there are some common problems with Mulliken and > Lowdin population analyses. In particular, they do > not > converge with expansion of the basis set, and they > may > give absurd results with basis sets including > diffuse > functions (like 6-311+G(3df)). You may try other > schemes, f.inst. the Natural Atomic Orbital analysis > which is usually much more satisfactory. Frank > Jensen's "Introduction to Computational Chemistry" > (Wiley) has a useful discussion of the various > approaches. > Yours, Jens >--< > > ------------------------------------------------------ > 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://www.ruc.dk/~~spanget > > ------------------------------------------------------ > Ding Xunlei ding . sissa.it wrote: > > Sent to CCL by: Ding Xunlei [ding#sissa.it] > Dear All, > Using Gaussian03 with the input file below, we can > get the Mulliken and > Lowdin charge populations on CO2 molecule. But the > results are totally > opposite, as: > Mulliken atomic charges: > 1 C 1.006159 (lose electrons) > 2 O -0.503080 > 3 O -0.503080 > Lowdin Atomic Charges: > 1 C -0.465607 (get electrons?) > 2 O 0.232804 > 3 O 0.232804 > Why? > Thank you! > Yours, > Ding > #pbepbe/6-311+G(3df) opt iop(6/80=1) > mp2 > 0 1 > C > O 1 1.16 > > O 1 1.16 2 180.0> > __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From owner-chemistry@ccl.net Tue Feb 14 17:20:00 2006 From: "Konstantin Kudin konstantin_kudin]|[yahoo.com" To: CCL Subject: CCL: Trace of the Quadrupole Message-Id: <-30895-060214164440-32290-8CYoqGM3wqANpczOnkKPNA*server.ccl.net> X-Original-From: Konstantin Kudin Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Tue, 14 Feb 2006 12:44:29 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Konstantin Kudin [konstantin_kudin[-]yahoo.com] Well, the reason is fairly straightforward (I think). The trace of the quadrupole moment is actually the spheropole moment [++=]. The spheropole moment is invariant with respect to rotations, whereas the other components are not. Then one is usually interested in the spheropole and the remaining traceless quadrupole components in different contexts, and so they are split like that. Konstantin --- "Don Steiger sd00_2002 .. yahoo.com" wrote: > Sent to CCL by: "Don Steiger" [sd00_2002. a .yahoo.com] > Quadrupole moments are generally defined in such a way as to make > them traceless. Multipole expansions can easily be done in such a > way that the trace of the quadrupole is non-zero. I was wondering if > there are specific reasons why chemist use the traceless form. > __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From owner-chemistry@ccl.net Tue Feb 14 22:28:00 2006 From: "Alfredo Mayall Simas simas- -ufpe.br" To: CCL Subject: CCL: Lanthanide parameters Message-Id: <-30896-060214191647-4776-eJ9s/Mp8/sWLLLm7VN7KNw/./server.ccl.net> X-Original-From: "Alfredo Mayall Simas" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 14 Feb 2006 20:35:11 -0300 MIME-Version: 1.0 Sent to CCL by: "Alfredo Mayall Simas" [simas|,|ufpe.br] Dear Sanjay, I do not know if that is what you need, but we have data on geometries of lanthanide complexes - they are somewhat larger than the systems you mentioned. Please let us know if that would be of interest to you. Perhaps you may also be interested in our Sparkle Model, designed to fast and accurately predict the geometries of lanthanide complexes. The Sparkle Model can be easily implemented in MOPAC93r2. For details, please visit http://www.sparkle.pro.br Sincerely, Alfredo M. Simas Recife, PE, Brazil ----- Original Message ----- Dear CCLers, Could anyone help me by giving the some of the lanthanide compounds molecular strucuture and the parameters like bond length, bond angle for various lanthanide and actinide compounds like laf3,la203,las,ceo2,ce203, etc. Any pointers or papers will be greatly helpful. regards, sanjay