From owner-chemistry@ccl.net Fri Oct 20 02:45:00 2006 From: "Orlin Blajiev blajiev+/-vub.ac.be" To: CCL Subject: CCL:G: queirs about molden programme Message-Id: <-32842-061020024226-3348-3uAomL2Zgi68d3Oumf20bA,+,server.ccl.net> X-Original-From: Orlin Blajiev Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 20 Oct 2006 08:44:11 +0200 MIME-Version: 1.0 Sent to CCL by: Orlin Blajiev [blajiev__vub.ac.be] You can also try xcrysden program. The picture quality is very good. Best Orlin Joydeep Chowdhury joydeep72_c ~ rediffmail.com wrote: > Sent to CCL by: "Joydeep Chowdhury" [joydeep72_c!^!rediffmail.com] > Dear Sir: > >> As a Molden user could you please enlighten me how to generate 2D >> contour maps of Molecular electrostatic potential from Gaussian >> output files or cube files. In this connection I must mention that I >> can generate 3D mesp isosurface from the Gaussian output cube file. >> Waiting eagerly for your reply >> Sincerely yours >> Dr Joydeep Chowdhury> > > > > -- Orlin Blajiev Department of Metallurgy, Electrochemistry and Materials Science Faculty of Applied Science Vrije Universiteit Brussel Pleinlaan 2, B-1050 Brussels Belgium http://www.vub.ac.be/META/ tel.: 32-(0)2-6293538 fax : 32-(0)2-6293200 From owner-chemistry@ccl.net Fri Oct 20 05:43:01 2006 From: "Arturo Robertazzi robertaz]![sissa.it" To: CCL Subject: CCL: Laplacian and AIM Message-Id: <-32843-061020043406-24071-rlFVhj5HFNWX/QapXKUYuA],[server.ccl.net> X-Original-From: Arturo Robertazzi Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Fri, 20 Oct 2006 09:35:36 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: Arturo Robertazzi [robertaz(_)sissa.it] Hi, if you are using the program AIM2000, that one that runs on windows...the explanation is easy. In that program what are you looking at is not the Laplacian, but L which is equal to -Laplacian! So that in this way you'll have: L>0, shared interactions such as covalent bonds L<0, closed-shell interactions, such as ionic, hydrogen bonds... ciao ciao On Thu, 19 Oct 2006, Mateusz Witkowski big_mateo[*]inbox.com wrote: > Sent to CCL by: Mateusz Witkowski [big_mateo a inbox.com] > Dear CCLers, > My question goes probably to those of you who works with the AIM2000 program. > > I'm trying to use this program in order to classify vdW interactions - mainly HBs. > As we know it is possible based on the generally accepted rules concerning the values of ED and its Laplacian at the BCPs. > > I've started with the test case - water dimer {mp2/6-31+G(d)}, since there is HB for sure, but I found a negative value of Laplacian. > In the literature, there are certain criteria for HB: > ED (0.002-0.035 au) > Laplacian (0.024-0.139 au) > > In my case these values are 0.029 and -0.023, respectively. ED is OK but Laplacian is not. > > Could anyone comment on that? What should be done, step by step? In the main menu I can choose between ED and Laplacian and obtain different values. Which of them should be taken in my case? > > I will appreciate your help. > TIA > Mateo> > > > -- Dr. Arturo Robertazzi INFM Democritos Center and International School for Advanced Studies (SISSA/ISAS) via Beirut 2-4 Trieste, 34014 Italy e-mail: robertaz%a%sissa.it phone: 040-3787-571 Home-Page: www.arturorobertazzi.blogspot.com From owner-chemistry@ccl.net Fri Oct 20 06:35:01 2006 From: "Patricia Lozano-Casal P.Lozano-Casal-$-ed.ac.uk" To: CCL Subject: CCL: GULP: predict and montecarlo Message-Id: <-32844-061019072646-1965-UGt1podhaaXxBSBoNzkyUQ(a)server.ccl.net> X-Original-From: Patricia Lozano-Casal Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format="flowed" Date: Thu, 19 Oct 2006 11:50:30 +0100 MIME-Version: 1.0 Sent to CCL by: Patricia Lozano-Casal [P.Lozano-Casal{:}ed.ac.uk] Dear all CCL subscribers, my question regards the use of GULP. I was wondering if any of you uses GULP for structure prediction (simulated annealing) and Monte Carlo purposes. I am having some problems setting up some calculations and I would really appreciate any help you can give me. I know that there are some examples in the GULP webpage, such as prediction using genetic algorithms, but they are not suitable for what I would like to run. So I was wondering if someone has a test file that I could use to test the method to predict structures using simulated annealing algorithms and to run MC simulations of liquids on a rigid system. Thank you very much for your time. Dr Patricia Lozano-Casal -- Dr Patricia Lozano-Casal Institute for Materials and Processes School of Engineering and Electronics University of Edinburgh Kenneth Denbigh Building The King's Buildings Mayfield Road Edinburgh, EH9 3JL, United Kingdom Phone: ++44 (0)131 650 4859 Fax: ++44 (0)131 650 6551 E-mail: P.Lozano-Casal^^^ed.ac.uk From owner-chemistry@ccl.net Fri Oct 20 07:10:00 2006 From: "Petrina Kamya kpetrina2[]yahoo.com" To: CCL Subject: CCL: Laplacian and AIM Message-Id: <-32845-061019142656-29752-h/982r25HND5dlc134li0w]|[server.ccl.net> X-Original-From: Petrina Kamya Content-Type: multipart/alternative; boundary="0-1665430869-1161278809=:22557" Date: Thu, 19 Oct 2006 10:26:49 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Petrina Kamya [kpetrina2:_:yahoo.com] --0-1665430869-1161278809=:22557 Content-Type: text/plain; charset=ascii Content-Transfer-Encoding: quoted-printable Hi Mateo,=0AWith AIM2000 you have to multiply the laplacian value by -4 to = get the proper value. There is a glitch in the program.=0APetrina=0A=0A=0A-= ---- Original Message ----=0AFrom: Mateusz Witkowski big_mateo[*]inbox.com = =0ATo: "Kamya, Petrina " =0ASent: Thursday, October 19, 2006 12:46:57 PM=0ASubject: CCL: Laplaci= an and AIM=0A=0ASent to CCL by: Mateusz Witkowski [big_mateo a inbox.com]= =0ADear CCLers,=0AMy question goes probably to those of you who works with = the AIM2000 program.=0A=0AI'm trying to use this program in order to classi= fy vdW interactions - mainly HBs. =0AAs we know it is possible based on the= generally accepted rules concerning the values of ED and its Laplacian at = the BCPs.=0A=0AI've started with the test case - water dimer {mp2/6-31+G(d)= }, since there is HB for sure, but I found a negative value of Laplacian.= =0AIn the literature, there are certain criteria for HB:=0AED (0.002-0.035 = au)=0ALaplacian (0.024-0.139 au)=0A=0AIn my case these values are 0.029 and= -0.023, respectively. ED is OK but Laplacian is not.=0A=0ACould anyone com= ment on that? What should be done, step by step? In the main menu I can cho= ose between ED and Laplacian and obtain different values. Which of them sho= uld be taken in my case?=0A=0AI will appreciate your help.=0ATIA=0AMateo=0A= =0A=0A=0A-=3D This is automatically added to each message by the mailing sc= ript =3D-=0ATo recover the email address of the author of the message, plea= se change=0Athe strange characters on the top line to the %% sign. You can a= lso=0A=0A=0AE-mail to = subscribers: CHEMISTRY%%ccl.net or use:=0A http://www.ccl.net/cgi-bin/c= cl/send_ccl_message=0A=0AE-mail to administrators: CHEMISTRY-REQUEST%%ccl.ne= t or use=0A=0A=0ASubsc= ribe/Unsubscribe: =0A=0A= =0A=0A=0AJob: http://= www.ccl.net/jobs =0AConferences: http://server.ccl.net/chemistry/announceme= nts/conferences/=0A=0ASearch Messages: http://www.ccl.net/htdig (login: cc= l, Password: search)=0A=0AIf your mail bounces from CCL with 5.7.1 error, c= heck:=0A=0A=0ARTFI: http://www.ccl.net= /chemistry/aboutccl/instructions/=0A=0A-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+= -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+=0A=0A=0A=0A=0A=0A=0A=0A=0A=0A --0-1665430869-1161278809=:22557 Content-Type: text/html; charset=ascii Content-Transfer-Encoding: quoted-printable
Hi Mateo,
With AIM2000 you have to multiply the = laplacian value by -4 to get the proper value. There is a glitch in the pro= gram.
Petrina


----- Original Message ----
From: Ma= teusz Witkowski big_mateo[*]inbox.com <owner-chemistry%%ccl.net>
To= : "Kamya, Petrina " <kpetrina2%%yahoo.com>
Sent: Thursday, = October 19, 2006 12:46:57 PM
Subject: CCL: Laplacian and AIM

Sent to CCL by: Mateusz Witkowski [big_mateo a inbox.com]
Dear CCLers,<= br>My question goes probably to those of you who works with the AIM2000 pro= gram.

I'm trying to use this program in order to classify vdW intera= ctions - mainly HBs.
As we know it is possible based on the generally accepted rules concer= ning the values of ED and its Laplacian at the BCPs.

I've started wi= th the test case - water dimer {mp2/6-31+G(d)}, since there is HB for sure,= but I found a negative value of Laplacian.
In the literature, there are= certain criteria for HB:
ED (0.002-0.035 au)
Laplacian (0.024-0.139 = au)

In my case these values are 0.029 and -0.023, respectively. ED i= s OK but Laplacian is not.

Could anyone comment on that? What should= be done, step by step? In the main menu I can choose between ED and Laplac= ian and obtain different values. Which of them should be taken in my case?<= br>
I will appreciate your help.
TIA
Mateo



-=3D Thi= s is automatically added to each message by the mailing script =3D-
To r= ecover 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.

E-mail to subscribers: CH= EMISTRY%%ccl.net or use:
      http://ww= w.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators:= CHEMISTRY-REQUEST%%ccl.net or use
      http://www.ccl.net/cgi-bin/ccl/send_ccl_message

Subscribe/Unsub= scribe:
      http://www.ccl.net/chemis= try/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job:= http://www.ccl.net/j= obs
Conferences: http:/= /server.ccl.net/chemistry/announcements/conferences/

Search Mess= ages: http://www.ccl= .net/htdig  (login: ccl, Password: search)

If your mai= l bounces from CCL with 5.7.1 error, check:
    &nbs= p; http:= //www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemi= stry/aboutccl/instructions/

-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+= -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+




<= /div>
--0-1665430869-1161278809=:22557-- From owner-chemistry@ccl.net Fri Oct 20 07:59:00 2006 From: "Tomasz Grabarkiewicz grabar(~)man.poznan.pl" To: CCL Subject: CCL: Laplacian and AIM Message-Id: <-32846-061020075409-16287-P6P68+IwZqitSuz5GIVBTA:_:server.ccl.net> X-Original-From: "Tomasz Grabarkiewicz" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-8859-2"; reply-type=original Date: Fri, 20 Oct 2006 13:53:54 +0200 MIME-Version: 1.0 Sent to CCL by: "Tomasz Grabarkiewicz" [grabar(a)man.poznan.pl] Hi Mateo, The L value in the AIM2000 program corresponds to the sum of KEG and KEK energies. Therefore the "true" value of Laplacian is -4L. It comes from the virial theorem. Since all critical points are classified according to the eigenvalues of the Hessian, than you can obtain the same value by summing them up. Hope this helps Tomasz From owner-chemistry@ccl.net Fri Oct 20 11:12:01 2006 From: "Leonardo De Maria ledm*novozymes.com" To: CCL Subject: CCL: CHARMM22 parameters for succinyl and p-nitroanilide terminal groups Message-Id: <-32847-061020110439-31061-wqbBvo1KvyyKDN6vxFYqyQ_-_server.ccl.net> X-Original-From: "Leonardo De Maria" Date: Fri, 20 Oct 2006 11:04:39 -0400 Sent to CCL by: "Leonardo De Maria" [ledm===novozymes.com] Hi, has anyone by chance developed parameters for succinyl and p-nitroanilide terminal groups compatible with CHARMM22? Regards, Leonardo From owner-chemistry@ccl.net Fri Oct 20 13:23:00 2006 From: "Xie Wang xie.wang.:.gmail.com" To: CCL Subject: CCL:G: questions about scrf calculation: ua0/uaff (gaussian) Message-Id: <-32848-061020101934-18295-biu6mXxyruqyiyLnuwqQDw_._server.ccl.net> X-Original-From: "Xie Wang" Date: Fri, 20 Oct 2006 10:19:33 -0400 Sent to CCL by: "Xie Wang" [xie.wang,+,gmail.com] Hello, I am trying to describe dissociation processes of a dimeric complex of small organic molecules in solution. Several questions: 1. what is the difference between UA0 and UAFF? Is there a reference that discussed the details of how those models are built? 2. gaussian output: "Error on total polarization charges = 0.01466" Is this the total error of the nuclear and electronic apparant charge? This number from UA0 model is about 10 times bigger than that from UAHF. Does this mean UAHF is more accurate? 3. Both UA0 and UAHF show this kind of output: Partition over spheres: Sphere on Atom Surface Charge GEl GCav GDR 1 C1 2.10 -0.022 -0.04 0.48 -0.13 2 C2 1.53 -0.014 -0.02 0.48 -0.15 3 C3 1.49 0.003 -0.09 0.63 -0.11 4 C4 1.69 0.002 -0.08 0.49 -0.11 5 C5 4.30 -0.028 0.21 1.23 -0.34 6 N6 17.24 0.096 -3.31 2.32 -1.44 7 C7 4.30 -0.028 0.21 1.23 -0.34 8 N8 17.24 0.096 -3.31 2.32 -1.44 9 C9 5.32 -0.037 0.28 1.23 -0.35 10 N10 17.53 0.097 -3.33 2.32 -1.45 11 C11 5.31 -0.037 0.28 1.23 -0.34 12 N12 17.53 0.097 -3.33 2.32 -1.44 13 C13 4.19 -0.005 0.17 1.24 -0.34 14 N14 17.80 0.176 -8.53 2.32 -1.46 15 C15 4.19 -0.005 0.17 1.24 -0.34 16 N16 17.80 0.176 -8.53 2.32 -1.53 17 C17 4.88 -0.008 0.24 1.24 -0.34 18 N18 17.80 0.177 -8.53 2.32 -1.46 19 C19 4.88 -0.008 0.24 1.24 -0.34 20 N20 17.80 0.177 -8.53 2.32 -1.46 Added spheres: 100.17 -0.030 -4.55 0.00 0.00 My first guess is that these are the exposed surface area/charge/free energy distributed over different atoms. However, these partitioned numbers do not add up to the number in the last line (Added spheres:...). So what do all these information mean? What is the relation of all these charges to the "Error on total polarization charges" (question 2)? 4 I have big difficulties to converge the geometries in solution (both in UA0 and UAHF). Even increase TSNUM to 300 I could only converge the geometries with "loose" criteria but not with the default convergence criteria. Can I use anything to further converge the geometry? Any information will be appreciated. Thanks in advance! From owner-chemistry@ccl.net Fri Oct 20 13:58:00 2006 From: "Rajan Vatassery r-vatassery+*+northwestern.edu" To: CCL Subject: CCL: Spherical Micelle Initial Guess (spatial reasoning problem) - SUMMARY Message-Id: <-32849-061020133539-24639-7O3wSFnkpEl1TK1t9Bau2A-,-server.ccl.net> X-Original-From: "Rajan Vatassery" Date: Fri, 20 Oct 2006 13:35:39 -0400 Sent to CCL by: "Rajan Vatassery" [r-vatassery,+,northwestern.edu] Thanks so much for your help, CCL. Here is a summary of this thread in case someone else needs to space particles equally on the surface of a sphere. 1. Sent to CCL by: laurent favaro [laurent.favaro(-)lpces.u-psud.fr] You could take fullerernes coordinates. C60 is spherical. There are two bond length, but very close. http://www.ccl.net/cca/data/fullerenes/index.shtml lf -- I would have used this if I were needing 60 particles, but unfortunately I needed about 100. alternatively, the platonic solids (which have up to 20 vertices I believe) are also valid possibilities. 2. Sent to CCL by: ReichertD]-[mir.wustl.edu Hi, You might check out the program Packmol by Martinez (Mart=EDnez, J. M.;= Mart=EDnez, L. Packing optimization for automated generation of complex= system's initial configurations for molecular dynamics and docking. J. Comp. Chem. 2003, 24, 819-825.) Binaries or maybe source code can be obtained from www.ime.unicamp.br/~martinez/packmol I hope that helps. -david David Reichert, Ph.D. Asst. Professor Radiology Washington University School of Medicine 510 S. Kingshighway, Campus Box 8225 St Louis, MO 63110 e-mail: reichertd!=!wustl.edu http://scoobie.wustl.edu/ voice: (314) 362-8461 fax: (314) 362-9940 -- I didn't try this, but I have the feeling I should have. 3. Sent to CCL by: Rajarshi Guha [rguha!A!indiana.edu] http://local.wasp.uwa.edu.au/~pbourke/geometry/spherepoints/ -- unfortunately, when i examine the source code posted on this web site, I see that the maximization will result in points that are off the sphere. I could be wrong, but I do not see a constraint to keep the particles on the surface of a sphere. I am not good at C so it is very possible this constraint is actually in the code, but I cannot be sure. 4. > From Richard Venable: I used random numbers to generate polar angles, and built multiple trial models with different random seeds. I packed loosely, expanding the radius, to reduce bad VDW contacts, esp. near the center of the sphere. The system will gracefully collapse with minimization and brief dynamics, esp. with explicit/implicit solvent. For the explicit solvent case, constant P dynamics is advised. Rick Venable 29/500 Membrane Biophysics Section NIH/NHLBI Lab. of Comp. Biology Bethesda, MD 20892-8014 U.S.A. (301) 496-1905 venabler AT nhlbi*nih*gov 5. > From Cory Pye: Hello, I seem to recall that this was discussed on the CCL when I was a postdoc with Tom Ziegler 1997-1999. I don't think that it was specifically related to micelles, and I recall a JCC paper as well. Of course, memory recall goes downhill after reaching 20... -Cory -- The specific paper is Rapid approximation to molecular surface area via the use of Boolean logic and look-up tables by Scott M. Le Grand, Kenneth M. Merz Jr. Journal of Computational Chemistry Volume 14, Issue 3 , Pages 349 - 352 Unfortunately they have not posted the code (this might be before online supplemental materials), and I figured that they might not have it anymore after 14 years. --- The end path I took was to generate a sphere with my own fortran code and then get a uniform spacing between the particles by minimizing the energy of sphere of particles with TINKER. I assigned equivalent charges (-.5) to each atom and I constrained one atom to the middle of a sphere (0,0,0) with the line RESTRAIN-POSITION 101 0.000 0.000 0.000 1001.0 in my .key file. Note that the "RESTRAIN-POSITION" entry in the TINKER manual has the incorrect syntax and that this is the correct syntax above (the force constant should be at the end). Then I restrained the distance between all the surface particles to be the radius of the sphere (10) with this line in the .key file: RESTRAIN-DISTANCE 101 1 100.0 10.0 10.01 where 101 and 1 are the two particular atoms I am constraining the distance between, 100.0 is the force constant, 10.0 and 10.01 are the distances the particle must be within. Of course you will need to add a line for each atom on the surface. Once again, the Ponder Lab helps out. Thanks for the input, Rajan rvatassery ( a ( yahoo dot // com From owner-chemistry@ccl.net Fri Oct 20 17:39:00 2006 From: "Mikael Johansson mikael.johansson{:}helsinki.fi" To: CCL Subject: CCL: Spherical Micelle Initial Guess (spatial reasoning problem) - SUMMARY Message-Id: <-32850-061020173338-5086-h/cEFrxCEm9B7ekYPGNW5A%a%server.ccl.net> X-Original-From: Mikael Johansson Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Fri, 20 Oct 2006 23:34:13 +0300 (EEST) MIME-Version: 1.0 Sent to CCL by: Mikael Johansson [mikael.johansson]![helsinki.fi] Hello Rajan and All! On Fri, 20 Oct 2006, Rajan Vatassery r-vatassery+*+northwestern.edu wrote: > Thanks so much for your help, CCL. Here is a summary of this thread in > case someone else needs to space particles equally on the surface of a > sphere. I've used the following short Mathematica procedure for getting points on a sphere. The number of points you can create is not continuous, though: Needs["Graphics`Polyhedra`"] n=17; kolmiot=Flatten[Geodesate[Polyhedron[Icosahedron],n][[1]]]; Export["test.txt", karjet=6.7953*Union[Flatten[Map[#[[1]]&,kolmiot],1]], "TSV"] The factor 6.7953 is the radius you want, n=17 controls the number of points on the surface. The procedure is not mine, I got it from Sampo Smolander. Have a nice day, Mikael J. http://www.iki.fi/~mpjohans/ From owner-chemistry@ccl.net Fri Oct 20 20:13:01 2006 From: "MolSoft Training andy|molsoft.com" To: CCL Subject: CCL: Workshop: Modern Drug Target Crystallography and Structure Based Drug Discovery Message-Id: <-32851-061020200326-19327-bWBoTAynOXOHqv1kOwkGxg(-)server.ccl.net> X-Original-From: MolSoft Training Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Fri, 20 Oct 2006 11:36:13 -0700 MIME-Version: 1.0 Sent to CCL by: MolSoft Training [andy(a)molsoft.com] Places are still available at a two day workshop on the cutting-edge developments in crystallography and structure-based drug design will be held on November 9th-10th, 2006 in La Jolla California. Registration and course content info here: http://ruppweb.dyndns.org/workshops/Molsoft_workshop.htm The workshop will be conducted by: Dr. Bernhard Rupp (Founder qed life science discoveries, inc) and Prof. Ruben Abagyan (Professor of Molecular Biology at The Scripps Research Institute and Founder of Molsoft LLC). The workshop entitled "Modern Drug Target Crystallography and Structure Based Drug Design" is suitable for executives, scientists, and technicians in the field of biological sciences, chemistry and drug discovery, who wish to expand their knowledge in the rapidly advancing field of high throughput drug target crystallography and structure guided drug discovery. The content of the workshop is designed for those who are considering using crystallography and virtual ligand screening as a tool in their drug discovery research and wish to get an overview of the techniques as well as for researchers already familiar with crystallography and in-silico, analysis, modeling and docking, who wish to learn more about the latest developments in this field. For more information please visit: http://ruppweb.dyndns.org/workshops/Molsoft_workshop.htm E mail andy]_[molsoft.com or call (858 625 2000 x108). Places are limited (12 participants) so early enrollment is encouraged.