From owner-chemistry@ccl.net Thu Jun 19 00:32:01 2008 From: "Kamalakar Jadhav kjadhav(_)vlifesciences.com" To: CCL Subject: CCL: Ploting protein-protein interactions Message-Id: <-37193-080619002445-15693-p9NN+L2qKbdgJjyeysvGiw#%#server.ccl.net> X-Original-From: Kamalakar Jadhav Content-Type: multipart/alternative; boundary="------------020607090509090402030601" Date: Thu, 19 Jun 2008 09:26:56 +0530 MIME-Version: 1.0 Sent to CCL by: Kamalakar Jadhav [kjadhav=vlifesciences.com] This is a multi-part message in MIME format. --------------020607090509090402030601 Content-Type: text/plain; charset=GB2312 Content-Transfer-Encoding: 7bit VLifeMDS software has the interaction viewer. It can show hydrogen bond, hydrophobic, pi stacking and steric interactions. Look at www.vlifesciences.com Hope this helps. Kamalakar --------------020607090509090402030601 Content-Type: text/html; charset=GB2312 Content-Transfer-Encoding: 7bit VLifeMDS software has the interaction viewer. It can show hydrogen bond, hydrophobic, pi stacking and steric interactions.
Look at www.vlifesciences.com

Hope this helps.

Untitled Document
Kamalakar
--------------020607090509090402030601-- From owner-chemistry@ccl.net Thu Jun 19 03:51:01 2008 From: "Michel PETITJEAN michel.petitjean===cea.fr" To: CCL Subject: CCL: rmsd calculation Message-Id: <-37194-080618184810-12200-fPNVwnI90/1JvIOgJRz+tg++server.ccl.net> X-Original-From: "Michel PETITJEAN" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 18 Jun 2008 23:55:31 +0200 MIME-Version: 1.0 Sent to CCL by: "Michel PETITJEAN" [michel.petitjean=-=cea.fr] I am afraid that Kabsch algorithm sometimes allows a mirror inversion. The pure rotation problem needs a quaternion method, as in ARMS = (mentioned in my previous posting): see appendix of my paper in J.Math.Phys, 1999,40(9),4587-4595. It has been extended to continuous and/or infinite sets: see appendix A.5 of my paper in J.Math.Phys. 2002,43(8),4147-4157. Michel Petitjean. http://petitjeanmichel.free.fr/itoweb.petitjean.shape.html ....................................................................... Sent to CCL by: Jerome Kieffer [jerome.Kieffer||terre-adelie.org] > I am looking for a (free) tool for calculating the RMSD between two = molecule conformations, preferably a script or command line tool as I = want to use it in batch mode. > It would be great if this tool also includes the possibility to do a = clustering. > > Perhaps, someone has a good suggestion. search for the Kabsch algorythm ... http://en.wikipedia.org/wiki/Kabsch_algorithm I implemented it in python for CAChe files, if you are intersted in. One tip for clustering: you can sort your vector-set by type of atoms and distance to the barycenter to overcome the limitation that your atoms could have diferent names (can be due to internal symmetries).=20 Best regards -- J=E9r=F4me KIEFFER : http://www.terre-adelie.org =C0 v=E9lo, prendre une rue =E0 contre-sens est moins dangeureux que prendre un boulevard dans le sens l=E9gal. =C0 qui la faute ? From owner-chemistry@ccl.net Thu Jun 19 05:40:00 2008 From: "Orlin Blajiev Orlin.Blajiev-,-vub.ac.be" To: CCL Subject: CCL:G: g03-Charges keyword Message-Id: <-37195-080619041051-23648-GIGYuCzkC9DeCGTO9S4Nrw[]server.ccl.net> X-Original-From: Orlin Blajiev Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 19 Jun 2008 09:21:41 +0200 MIME-Version: 1.0 Sent to CCL by: Orlin Blajiev [Orlin.Blajiev!A!vub.ac.be] Hi anybody, Could you please let me know what are the units for the field and electron repulsion parameters for the group called with CHARGE keyword in Gaussian. Best regards, Orlin -- Orlin Blajiev Department Materials and Chemistry(MACH)/Research Group META Vrije Universiteit Brussel Pleinlaan 2 - B 1050 Brussels - Belgium tel: 32 2 6293538 (secr. 3255) fax: 32 2 6293200 mail: blajiev-#-vub.ac.be http://www.vub.ac.be/META From owner-chemistry@ccl.net Thu Jun 19 07:10:01 2008 From: "gnli gnli~~dicp.ac.cn" To: CCL Subject: CCL: free code for Monte Carlo Message-Id: <-37196-080619052816-28435-0v9w3FncpZbswS+Htd4IlA(-)server.ccl.net> X-Original-From: "gnli" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0014_01C8D231.E8D73EB0" Date: Thu, 19 Jun 2008 17:28:36 +0800 MIME-Version: 1.0 Sent to CCL by: "gnli" [gnli:dicp.ac.cn] This is a multi-part message in MIME format. ------=_NextPart_000_0014_01C8D231.E8D73EB0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Dear CCLer, Anyone can provide some free softwares for monte carlo search for stable conformations under absolute configuration. The easier to learn the better. Many thanks in advance! best wishes Guanna Li gnli^^^dicp.ac.cn ------=_NextPart_000_0014_01C8D231.E8D73EB0 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Dear = CCLer,

Anyone can provide some free softwares for monte carlo search for stable conformations under absolute configuration. The easier to learn the = better.

Many thanks in advance! =

 

best wishes
Guanna Li
gnli^^^dicp.ac.cn



 

------=_NextPart_000_0014_01C8D231.E8D73EB0-- From owner-chemistry@ccl.net Thu Jun 19 07:48:01 2008 From: "Ghislain Deslongchamps ghislain__UNB.ca" To: CCL Subject: CCL: charge model for N-H in amides Message-Id: <-37197-080618164034-2684-cAKo4cL0exNZdJx2Vyy2nQ_._server.ccl.net> X-Original-From: Ghislain Deslongchamps Content-Type: multipart/alternative; boundary=Apple-Mail-2--712628642 Date: Wed, 18 Jun 2008 16:36:12 -0300 Mime-Version: 1.0 (Apple Message framework v924) Sent to CCL by: Ghislain Deslongchamps [ghislain:UNB.ca] --Apple-Mail-2--712628642 Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Content-Transfer-Encoding: 7bit Hello all, We have been using MMFF94x and RESP charges to model H-bonded host- guest complexes, including some containing amides of various N-H acidities. RESP doesn't seem to give the expected trend of increasing partial positive charge on NH hydrogen when going from CH3CONHR to CCl3CONHR to CF3CONHR. Other charge models, including Mulliken, AM1, AM1-BCC, PM3, MNDO, and ESP, also fail to give the expected trend. Any suggestions? Cheers, Ghislain Deslongchamps --Apple-Mail-2--712628642 Content-Type: text/html; charset=US-ASCII Content-Transfer-Encoding: quoted-printable Hello = all,

We have been using MMFF94x and RESP charges to = model H-bonded host-guest complexes, including some containing amides of = various N-H acidities. RESP doesn't seem to give the expected trend of = increasing partial positive charge on NH hydrogen when going from = CH3CONHR to CCl3CONHR to CF3CONHR. Other charge models, including = Mulliken, AM1, AM1-BCC, PM3, MNDO, and ESP, also fail to give the = expected trend. Any = suggestions?

Cheers,

Ghislain Deslongchamps


 =

= --Apple-Mail-2--712628642-- From owner-chemistry@ccl.net Thu Jun 19 09:11:00 2008 From: "Roberto Peverati peverati^_^oci.uzh.ch" To: CCL Subject: CCL:G: Frequency Vs Hessian Message-Id: <-37198-080618192416-17858-4bm8XK9cdcXkUxY/HZw0zw : server.ccl.net> X-Original-From: Roberto Peverati Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; format=flowed; delsp=yes Date: Thu, 19 Jun 2008 00:51:05 +0200 Mime-Version: 1.0 (Apple Message framework v924) Sent to CCL by: Roberto Peverati [peverati[#]oci.uzh.ch] Hello Antonio There are absolutely no differences between a frequency calculation in =20= gaussian and a hessian calculation in (PC-) GAMESS. Both these =20 keywords perform a second derivative analysis on the geometry you =20 specified in your input. To do the second derivative with GAMESS actually you have the choice =20 between 3 different method: the two that you mentioned - analytic and =20= numeric - plus semi-numeric. These terms refers to the method used to =20= make the derivative of the energy with respect to coordinates. Numeric (or better, full-numeric) means that gamess calculates the =20 energy at the stationary point (x,y,z), plus energies at some points =20 around it: (x+dx,y,z), (x-dx,y,z), (x,y+dy,z), (x,y-dy,z) and so on, I =20= think you got the idea... This is to get the numeric 1st derivative. =20 The same happens at every point calculated above, to have the 2nd =20 derivative. You can imagine now that this will require a lot of =20 computation cost, since the number of single point calculation that =20 you need are in order 6*6*N =3D 36*N, where N is the umber of atoms of =20= your molecule. The value of the displacement is the value of the step =20= you take (namely dx), so in principle it should be as much smaller as =20= possible, but in practice we must take a good compromise to consider =20 the curvature of your PES (the default is usually very good). Semi-numeric is actually the default method for all DFT calculations =20 and uses the analytic form of the 1st derivative (which is the =20 gradient), and a numeric derivation for the 2nd derivative. It is much =20= cheaper because it needs only 6*N calculations, but it is available =20 only for those method that have the gradient implementation (for =20 example R/UHF, DFT, but not CISD) Analytic requires the analytic gradient and the analytic second =20 derivative implementations. It is available for some method (R/UHF), =20 and requires only 1 calculation of the energy, since the rest is done =20= analytically. For you might be interesting to know that in almost all the cases the =20= 3 method will provide the same numerical results, so you don't have to =20= struggle a lot in the choice of it and, as I said, 0.01 is almost =20 always a very good number for displacement. In my experience, analytic is always the best choice, but for many =20 method it is not available (e.g. DFT). Therefore semi-numeric is very =20= good and provide results in a reasonable amount of time. On the other =20= side, full-numeric must be used only if none of the previous methods =20 are available, since it is really really demanding and for large =20 molecules it is almost impossible to use. I hope this will help, and excuse me if I've been too long... Roberto ----------------------------------------------------------- Roberto Peverati OCI - Institute of Organic Chemistry Universit=E4t Z=FCrich Winterthurerstrasse 190 8057 Z=FCrich, Switzerland ----------------------------------------------------------- On Jun 18, 2008, at 9:28 PM, Antonio G De Crisci =20 antonio.decrisci[*]utoronto.ca wrote: > > Sent to CCL by: "Antonio G De Crisci" [antonio.decrisci^^^utoronto.ca] > Hello, > > Can somebody tell me the difference between a frequency calculation =20= > in Gaussian compared to a hessian calculation (with vibrational =20 > analysis) in PC GAMESS? > > Also, in GAMESS, when performing a hessian, I have two method =20 > options: numeric or analytic. When I choose the numeric size, I have =20= > an option of changing the displacement size. What is the difference =20= > between the two, and what value of the displacement size (default=3D =20= > 0.01) would be suitable for a B3LYP/6-311G. > > Thanks, > Antonio De Crisci > University of Toronto > > > > -=3D This is automatically added to each message by the mailing script = =20 > =3D- > To recover the email address of the author of the message, please =20 > change> Conferences: http://server.ccl.net/chemistry/announcements/=20 > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: =20 > search)> > From owner-chemistry@ccl.net Thu Jun 19 09:45:00 2008 From: "Michael Kullman mjkullman%wichita.edu" To: CCL Subject: CCL:G: AMD Phenom vs. Intel Quad Q6600 Message-Id: <-37199-080619082904-11558-XWXgvD4UZrdoGA5ohIEz0g[#]server.ccl.net> X-Original-From: "Michael Kullman" Date: Thu, 19 Jun 2008 08:29:00 -0400 Sent to CCL by: "Michael Kullman" [mjkullman:wichita.edu] I have been working with Gaussian on the AMD quadcore problem since last year. The problem was the b2 chips ie 9600, 9700, etc. The new b3 chips 9X50 have tested fine on all my machines. I have a system with a b3 9850 running under Suse 10.3 64-bit and it runs Gaussian in parallel using all four cores. I had an 9700 ie b2 and yes there was a problem most likely caused by the TLB bug. As far as the performance difference, it is somewhat subject to the systems that are being worked with. However with that said, using a std benchmark, the q6600 does out performance an 9850 with Rev E Gaussian under Suse Linux 10.3. This is based on an average of 5 q6600 machines and three AMD quad core machines ( 9850s and 9650 oced ). However once one scales to a quad socket vs quad socket, the AMD Opteron quads out performs the Intel Xeon. For single socket the Intel Q6600 is your best bet at this time. Best of Luck Michael From owner-chemistry@ccl.net Thu Jun 19 11:38:00 2008 From: "zhendong zhao zzhao||olemiss.edu" To: CCL Subject: CCL:G: AMD Phenom vs. Intel Quad Q6600 Message-Id: <-37200-080619112843-24943-Tntlhwe1zdxcQZPpCw0nvQ,+,server.ccl.net> X-Original-From: zhendong zhao Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII Date: Thu, 19 Jun 2008 10:28:28 -0500 Mime-Version: 1.0 Sent to CCL by: zhendong zhao [zzhao(~)olemiss.edu] Hi Michael, I have a box, configred with phenom 9850 (which should be b3 stepping), and MB ASUS M3A-H/HDMI. The configuaration is never stable under parallel calculations. I also use SUSE 10.3. Would you give more information about your motherboard? I would like to buy this MB, replace the current one, and let the AMD box run smoothly. If you make some specific changes to SUSE configurations, please also make some comments. Appreciate your help. ZZ On Thu, 19 Jun 2008 08:29:00 -0400 "Michael Kullman mjkullman%wichita.edu" wrote: > > Sent to CCL by: "Michael Kullman" [mjkullman:wichita.edu] > > > I have been working with Gaussian on the AMD quadcore problem since > last year. The problem was the b2 chips ie 9600, 9700, etc. The new > b3 chips 9X50 have tested fine on all my machines. I have a system > with a b3 9850 running under Suse 10.3 64-bit and it runs Gaussian in > parallel using all four cores. I had an 9700 ie b2 and yes there was > a problem most likely caused by the TLB bug. As far as the > performance difference, it is somewhat subject to the systems that > are being worked with. However with that said, using a std > benchmark, the q6600 does out performance an 9850 with Rev E Gaussian > under Suse Linux 10.3. This is based on an average of 5 q6600 > machines and three AMD quad core machines ( 9850s and 9650 oced ). > However once one scales to a quad socket vs quad socket, the AMD > Opteron quads out performs the Intel Xeon. For single socket the > Intel Q6600 is your best bet at this time. > > Best of Luck > > Michael > > > > -= 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> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > From owner-chemistry@ccl.net Thu Jun 19 14:53:01 2008 From: "Cesar Millan pachequin[A]gmail.com" To: CCL Subject: CCL: DNA structure modification software Message-Id: <-37201-080619145159-21446-gTFjY/jBE/pKXL9RFB0YNA,,server.ccl.net> X-Original-From: "Cesar Millan" Date: Thu, 19 Jun 2008 14:51:55 -0400 Sent to CCL by: "Cesar Millan" [pachequin.:.gmail.com] Hi everyone, Does any one knows some free software (running in linux) that could modify DNA or protein residues like in Insight using Biopolymer module? I would like to generate mutants of crystallographic structures but preserving, the most, the original geometrical parameters of each residue mutated. Any suggestion will be appreciate. Best. From owner-chemistry@ccl.net Thu Jun 19 15:35:00 2008 From: "zohreh karimzadeh zohrehkarimzadeh(0)yahoo.com" To: CCL Subject: CCL: ewld code check in fortran Message-Id: <-37202-080619101541-1706-hG58VXazQpuDwbExVCaUvw,server.ccl.net> X-Original-From: "zohreh karimzadeh" Date: Thu, 19 Jun 2008 10:15:37 -0400 Sent to CCL by: "zohreh karimzadeh" [zohrehkarimzadeh^^^yahoo.com] Dear All I try to run NVT simulation in MC by fortran(108 ion (charhed hard sphere) +,-) . I have problem in Ewald potential calculation. In my code real part of the potential dont converge. Could possibly any one guid me. this is my code for real part: SUBROUTINE REALCHANGEe use const use matrix use MSIMSL POTREALINITIAL=0.0 POTREALFINAL=0.0 ROSTAR=6.0*HARDPACK/PIE VOLRED=NIONS/ROSTAR H=0.5*(VOLRED)**(1.0/3.0) DO 19 M=1,NIONS IF(M.NE.IPART)THEN RX=X(Ipart)-X(M) RY=Y(Ipart)-Y(M) RZ=Z(Ipart)-Z(M) RX=RX-2.0*INT(RX) RY=RY-2.0*INT(RY) RZ=RZ-2.0*INT(RZ) RSQ=RX*RX+RY*RY+RZ*RZ RSQROOT=SQRT(RSQ) ARGERFC=ALPHA*RSQROOT POTTERM=CHARGE(IPART)*CHARGE(M) POTTERM=POTTERM*ERFC(ARGERFC)/(RSQROOT*H) POTREALINITIAL=POTREALINITIAL+POTTERM RX=XT-X(M) RY=YT-Y(M) RZ=RZ-Z(M) RX=RX-2.0*INT(RX) RY=RY-2.0*INT(RY) RZ=RZ-2.0*INT(RZ) RSQ=RX*RX+RY*RY+RZ*RZ RSQROOT=SQRT(RSQ) ARGERFC=ALPHA*RSQROOT POTTERM=CHARGE(IPART)*CHARGE(M) POTTERM=POTTERM*ERFC(ARGERFC)/(RSQROOT*H) POTREALFINAL=POTREALFINAL+POTTERM END IF 19 CONTINUE POTREALINITIAL=POTREALINITIAL*REDBJERRUM POTREALFINAL=POTREALFINAL*REDBJERRUM REALCHANGE=POTREALFINAL-POTREALINITIAL END SUBROUTINE REALCHANGEE From owner-chemistry@ccl.net Thu Jun 19 16:46:01 2008 From: "Mauricio Esguerra esguerra_._rci.rutgers.edu" To: CCL Subject: CCL: DNA structure modification software Message-Id: <-37203-080619161733-32382-9T+6zVdGjObpWNsfrNtXYg[*]server.ccl.net> X-Original-From: Mauricio Esguerra Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Thu, 19 Jun 2008 15:38:22 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: Mauricio Esguerra [esguerra(0)rci.rutgers.edu] Hello Cesar, You can use the rebuild utility from 3DNA. http://dnaserver.rutgers.edu/software.php You just need a the original x-ray pdb structure and from that one you run: find_pair original.pdb stdout | analyze a bp_step.par file will be created. You just have to edit this file and mutate to whichever base-pairs you want. after modification (mutation) of the bp_step file you just run: rebuild -atomic bp_step.par mutated.pdb Best Regards, +++++++++++++++++++++++++++++++++++++++++++++++ + Mauricio Esguerra Neira + + T.A. and Graduate Student + + Wilma K. Olson Group + + Chemistry and Chemical Biology Department + + Rutgers, The State University of New Jersey + + Phone Number: 732-445-4619 + + Email: esguerra-x-eden.rutgers.edu + +++++++++++++++++++++++++++++++++++++++++++++++ On Thu, 19 Jun 2008, Cesar Millan pachequin[A]gmail.com wrote: > > Sent to CCL by: "Cesar Millan" [pachequin.:.gmail.com] > Hi everyone, Does any one knows some free software (running in linux) that could modify DNA or protein residues like in Insight using Biopolymer module? I would like to generate mutants of crystallographic structures but preserving, the most, the original geometrical parameters of each residue mutated. > > Any suggestion will be appreciate. > > Best.> > > From owner-chemistry@ccl.net Thu Jun 19 17:20:01 2008 From: "Elaine Meng meng . cgl.ucsf.edu" To: CCL Subject: CCL: DNA structure modification software Message-Id: <-37204-080619160255-10612-fwbd616JxCCIVBSj8pwLhQ{=}server.ccl.net> X-Original-From: "Elaine Meng" Date: Thu, 19 Jun 2008 16:02:51 -0400 Sent to CCL by: "Elaine Meng" [meng[*]cgl.ucsf.edu] Hi Cesar, You might want to try the "swapaa" (amino acid) and "swapna" (nucleic acid) commands in UCSF Chimera. There is also a tool with a graphical interface, Rotamers (amino acids only). I don't know if these would preserve the original conformation to your liking, but you could also open another copy of the original structure and rotate the bonds in the new residues to match. Chimera is free for noncommercial use and can be downloaded for several platforms including linux. Normally I recommend the latest production release, but it is currently rather old (last fall, so we are planning another soon), so for now a newer snapshot or daily build is probably better: http://www.cgl.ucsf.edu/chimera/download.html#snapshots http://www.cgl.ucsf.edu/chimera/alpha-downloads.html Some related documentation: swapaa and swapna commands, Rotamers tool, a tutorial that rotates bonds and uses Rotamers: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/swapna.html http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/framerot.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html Best, Elaine ----- Elaine C. Meng, Ph.D. meng-x-cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html