From owner-chemistry@ccl.net Mon Jun 1 04:48:00 2009 From: "Jerome Kieffer jerome.Kieffer::terre-adelie.org" To: CCL Subject: CCL:G: Moving Gaussian executables from one machine to another Message-Id: <-39406-090601040256-31786-3hQ1sqbLGWEkS64JajNzDQ/a\server.ccl.net> X-Original-From: Jerome Kieffer Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-15 Date: Mon, 1 Jun 2009 10:02:43 +0200 Mime-Version: 1.0 Sent to CCL by: Jerome Kieffer [jerome.Kieffer%x%terre-adelie.org] > >=20 > > echo 0 > /proc/sys/kernel/randomize_va_space > >=20 > > and try again.=20 >=20 > That did indeed fix it after a bit of a struggle. I had to su to root to= =20 > do it. It would not allow me to use sudo. >=20 > So all is well. Googling suggested that I should add this line to=20 > /etc/rc.local to make sure it happens every time I reboot. >=20 > However, this is just magic to me. I do not have a clue what is going=20 > on. Could you or anybody please explain it so we can all become a bit wis= er? Since more or less linux-kernel 2.6, for security reason, the linux kernel is randomizing memory page for allocation, this is to prevent a program B to accessing memory of a program A. As Gaussian'98 and 03 are in F77 with only static memory allocation, the trick (ugly) was to allocate memory in C and to make it use by F77 programs, you see the problem if memory pages are not one after the other.=20 To make it permenent, either pass the option "norandmaps" to the kernel or append it to you /boot/grub/menu.lst with the other kernel option, it will be taken into account at next boot. Either append the option in the file : /etc/sysctrl.conf and run=20 sysctrl -p Of course everything as root as we are playing with the kernel. > > Gaussian is an old code (F77) being less and less > > compatible with the new style of coding of Linux (allocating pages > > here). I guess evolution will occure, either by an update to fit modern > > computer programming style, either in the the darwin sens. >=20 > While I understand this, I think you are not really quite correct.=20 > Modern compilers can handle F77 quite well, although they are perhaps a=20 > bit more picky than some older compilers. The problem is not F77 but the way F77 allows memory allocation. > The problem, in my opinion=20 > with Gaussian, is the C code not the F77 code. The error I give above=20 > comes from C routine ntrext1 in g98/bsd/mdutil.c. The C code there is=20 > really old fashioned in G98 and talking to people who have compiled G03,= =20 > it is not much better there. I do not have access to the G03 code. gcc4=20 > gives a whole mass of warnings when compiling g98 mdutil.c and the=20 > Gaussian approved pgf77 compiler for i386 target requires gcc for=20 > mdutil. It is not clear to me that G98 can be compiled correctly unless=20 > you have a very old gcc3 compiler. Has anyone used gcc4 and pgf77 with g9= 8? gcc3.4 is still maintained but more likely, you will need the good old permissive gcc2.95 or 2.96. > One of you suggested the intel ifort compiler. I am not sure that it is=20 > free for individual use. It is also not supported by Gaussian Inc for=20 > i386 compiles of G98. I will however investigate it. Intel compilers are free for personal use, but unless you are very good at both Fortran and C programming, the compilation is far from being straight forwards (but not impossible) Hope this helps --=20 J=E9r=F4me KIEFFER =20 http://www.terre-adelie.org From owner-chemistry@ccl.net Mon Jun 1 05:48:00 2009 From: "kadir kadir{=}visual1.chem.pitt.edu" To: CCL Subject: CCL: New code for vibrational modeling Message-Id: <-39407-090601054412-2165-uxeua0kMYjpkk31niygfAQ!A!server.ccl.net> X-Original-From: kadir Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 01 Jun 2009 02:44:02 -0700 MIME-Version: 1.0 Sent to CCL by: kadir [kadir^visual1.chem.pitt.edu] Apologies for cross posting... Dear Colleagues, A new program for solving vibrational problems is available for download: http://iopenshell.usc.edu/downloads/ezvibe/ The program is available as an executable which can be used with any of the symmetrized polynomial PESs of Braams et al [see JPC 122, 044308 (2005)], many of which can be downloaded from: http://iopenshell.usc.edu/downloads/ezpes. Best regards, kadir ---------- Kadir Diri, PhD Research Scientist Department of Chemistry and iOpenShell Center SSC #401 University of Southern California Los Angeles, CA 90089-0482 -------------------------- Relativistic correction to Murphy's law: Whether things can go wrong or not, depends on your frame of reference. From owner-chemistry@ccl.net Mon Jun 1 06:23:00 2009 From: "kadir kadir|visual1.chem.pitt.edu" To: CCL Subject: CCL: PES library available for download Message-Id: <-39408-090601054919-4315-ebxxA2u5X2ktZIVTsOl+iQ**server.ccl.net> X-Original-From: kadir Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 01 Jun 2009 02:49:12 -0700 MIME-Version: 1.0 Sent to CCL by: kadir [kadir- -visual1.chem.pitt.edu] Dear Colleagues, A library of full-dimensional semi-global potential energy surfaces (PES) generated from ab initio calculations is available for download: http://iopenshell.usc.edu/downloads/ezpes/ The library (ezPES) contains pre-compiled binaries and PES data files, and can be easily integrated into your own program, e.g., for dynamics or spectroscopy calculations. Currently, the following PESs are available: C2H3, C3H2 (singlet and triplet), H4CF, HCOH+, HCOH, C2H2, CH3OH, H2CO, H3O2-, H3O+, H5O2+. We will be adding others as they become available. Enjoy! kadir ---------- Kadir Diri, PhD Research Scientist Department of Chemistry and iOpenShell Center SSC #401 University of Southern California Los Angeles, CA 90089-0482 -------------------------- Relativistic correction to Murphy's law: Whether things can go wrong or not, depends on your frame of reference. From owner-chemistry@ccl.net Mon Jun 1 10:08:00 2009 From: "cleophas wawire muhavini__yahoo.com" To: CCL Subject: CCL:G: Missing ZINDO/S parameters for atomic number 44. Message-Id: <-39409-090528122313-25427-JNfsBtS0GKXNRP8Fscb4Qg:_:server.ccl.net> X-Original-From: cleophas wawire Content-Type: multipart/alternative; boundary="0-1938173342-1243524182=:59484" Date: Thu, 28 May 2009 08:23:02 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: cleophas wawire [muhavini::yahoo.com] --0-1938173342-1243524182=:59484 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hallo, Could someone kindly help me to put=0Athe ruthenium parameters in the ZIND= O/S gaussian. =0A=0AI am trying to calculate the absorption=0Aspectra of Ru= thenium complexes without success. =0A=0APart of my input file for =0A[Ru(b= py)3]2+ reads as follows:=0A =0A=0A%chk=3DRuBpy3-zindo.chk =0A=0A =0A=0A#p zindo=3D(window=3D(100,188), 50-50)=0A =0A=0Aand the output file contained the=0Afollowing =0A=0A =0A=0A One-electron integrals computed=0Ausing PRISM.=0A=0A Generate ZINDO/= S integrals.=0A=0A Missing ZINDO/S parameters for=0Aatomic number 44.=0A =0A=0A I=0Ahave seen that it is actually possible to do a ZINDO study as=0A= reported in the work below:=0A =0A=0ASynthesis,=0ASpectroscopic and a ZINDO study of cis-=0Aand trans-(X2)= Bis(4,4'-dicarboxylic=0Aacid-2,2'-bipyridine)Ruthenium(II) Complexes (X =3D= Cl-, H2O,=0ANCS-)=0A=0A My specific question is; how do I ensure there are ZINDO/S parameters for= =0Aatomic number 44 (for Ru)? Thanking you in advance. Muhavini. =A0 =0A=0A=0A --0-1938173342-1243524182=:59484 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Hallo,
Could someone kindly help me to pu= t=0Athe ruthenium parameters in the ZINDO/S gaussian. =0A=0A

I am trying to calculate the absorption=0Aspectra of Ruth= enium complexes without success. =0A

=0A

Part of my input file for =0A[Ru(bpy)3]2+ reads a= s follows:

=0A


=0A

=0A

%chk=3DRuBpy3-zindo.chk =0A

=0A


=0A

=0A


=0A

=0A

and the output = file contained the=0Afollowing =0A

=0A

=
=0A

=0A

One-electron integrals c= omputed=0Ausing PRISM.=0A

=0A

Ge= nerate ZINDO/S integrals.=0A

=0A

Missing ZINDO/S parameters for=0Aatomic number 44.

=0A


=0A

=0A

I=0Ahave seen that it is actually possible to do a ZINDO study as= =0Areported in the work below:

=0A

Synthesis,=0ASpectroscopic and a ZINDO study of <= /font>cis= -=0Aand trans-(X2)Bis(4,4'-dicarboxylic=0Aacid-2,2'-bipyridine)Ruthenium(II) C= omplexes (X =3D Cl-, H2<= b>O,=0ANCS-)=0A=0A


My specific question is; how d= o I ensure there are ZINDO/S parameters for=0Aatomic number 44 (for Ru)?Thanking you in advance.
Muhavini.
 

=0A= =0A --0-1938173342-1243524182=:59484-- From owner-chemistry@ccl.net Mon Jun 1 10:43:01 2009 From: "Kshatresh Dutta Dubey kshatresh++gmail.com" To: CCL Subject: CCL: Software to calculate IC50 value Message-Id: <-39410-090601082114-5687-+levQvfSkSHQQiSC9EbEag!=!server.ccl.net> X-Original-From: Kshatresh Dutta Dubey Content-Type: multipart/alternative; boundary=0016364ee01c2e5926046b47c9d2 Date: Mon, 1 Jun 2009 17:02:48 +0530 MIME-Version: 1.0 Sent to CCL by: Kshatresh Dutta Dubey [kshatresh%a%gmail.com] --0016364ee01c2e5926046b47c9d2 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi, Can anyone tell me about any free software that calculates IC50 values from binding energy or theoretical data? Any help will be heartly appreciated. Thanks In advance. Regards Kshatresh Dutta Dubey --0016364ee01c2e5926046b47c9d2 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hi,
Can anyone tell me about any =A0free soft= ware that calculates IC50 values from binding energy or theoretical data?
Any help will be heartly appreciated.
Thanks In advance.
Regards
K= shatresh Dutta Dubey
--0016364ee01c2e5926046b47c9d2-- From owner-chemistry@ccl.net Mon Jun 1 13:05:01 2009 From: "TJ O Donnell tjo-#-acm.org" To: CCL Subject: CCL: PES library available for download Message-Id: <-39411-090601125901-17817-oj7Mg8XXulgAHnqT96mKKw/a\server.ccl.net> X-Original-From: "TJ O'Donnell" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 01 Jun 2009 09:58:53 -0700 MIME-Version: 1.0 Sent to CCL by: "TJ O'Donnell" [tjo#,#acm.org] This looks very useful. I don't have the Intel compiler and the library looks to be incompatible with gcc/g++. Is there a g++ comatible ezPES library available? TJ O'Donnell kadir kadir|visual1.chem.pitt.edu wrote: > > Sent to CCL by: kadir [kadir- -visual1.chem.pitt.edu] > Dear Colleagues, > > A library of full-dimensional semi-global potential energy surfaces > (PES) generated from ab initio calculations is available for download: > http://iopenshell.usc.edu/downloads/ezpes/ > > The library (ezPES) contains pre-compiled binaries and PES data files, > and can be easily integrated into your own program, e.g., for dynamics > or spectroscopy calculations. > > Currently, the following PESs are available: C2H3, C3H2 (singlet and > triplet), H4CF, HCOH+, HCOH, C2H2, CH3OH, H2CO, H3O2-, H3O+, H5O2+. We > will be adding others as they become available. > > Enjoy! > kadir > > > ---------- > Kadir Diri, PhD > Research Scientist > Department of Chemistry and iOpenShell Center > SSC #401 > University of Southern California > Los Angeles, CA 90089-0482 > -------------------------- > > Relativistic correction to Murphy's law: > Whether things can go wrong or not, depends on your frame of reference.http://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > From owner-chemistry@ccl.net Mon Jun 1 14:05:00 2009 From: "Yves Wang yves.wang()duke.edu" To: CCL Subject: CCL:G: NBODel for Gaussian 03 Message-Id: <-39412-090601124134-16123-ZZUaOR/37qPlcRLMojZ5sg###server.ccl.net> X-Original-From: Yves Wang Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=GB2312 Date: Mon, 01 Jun 2009 12:10:19 -0400 MIME-Version: 1.0 Sent to CCL by: Yves Wang [yves.wang _ duke.edu] Hi all, I have been having a lot of troubles running $NBODel with G03. The (IOp(5/48=10000)) seems to be fixed and I can now finally get some simulations running. Now my problem is about the geometry optimization with NBODel. The simulation runs without error. However, there is no "optimized geometry/parameter" stored in the log file. Although I can monitor the energy as the simulation goes on, but I couldn't get any information about the geometry of the system. Here's the input file: %mem=300MB %nproc=2 # B3LYP/AUG-cc-pVTZ Opt POP=NBODel # IOp(6/7=3) SCRF=(PCM,Solvent=Water) # Gfinput Test Units(Ang,Deg) 3 waters optimization with NBOdel 0 1 H O,1,B1 H,2,B2,1,A1 O,2,B3,1,A2,3,D1,0 H,2,B4,1,A3,4,D2,0 H,2,B5,1,A4,4,D3,0 H,2,B6,1,A5,4,D4,0 O,2,B7,1,A6,4,D5,0 H,4,B8,2,A7,1,D6,0 Variables: B1=0.97544021 B2=1.89813098 B3=2.87085105 B4=0.97542882 B5=1.89863545 B6=3.29147464 B7=2.87124809 B8=0.97063133 A1=110.4674383 A2=109.63474112 A3=104.88409751 A4=110.07609521 A5=111.26444883 A6=109.91300517 A7=107.1786031 D1=-0.6832864 D2=-117.91242371 D3=123.43991477 D4=107.14383726 D5=124.56982752 D6=138.83484765 $NBO file=dfe_c $END $DEL delete 2 orbitals 273 275 $END I tried to change the route card, IOp, #p, Pop=(full, nbodel) and many things, but I still could not get optimized geometry. Has anyone got similar issues before? Thanks in advance for your reply. Best, -- Yi(Yves) Wang Department of Biochemistry Structural Biology & Biophysics Program Duke University BS: University of Science and Technology of China School of Life Sciences, National Laboratory for Physical Sciences at Microscale Tel: +1-919-236-3307 (Cell) +1-919-684-0235 (Lab 1) +1-919-660-1634 (Lab 2) Office: A20 LSRC / 5301 FFSC E-Mail: yves.wang]_[duke.edu Mail: Box 90317, Chemistry Department From owner-chemistry@ccl.net Mon Jun 1 15:57:01 2009 From: "Farhan Pasha pashafa|a|yahoo.co.in" To: CCL Subject: CCL: Software to calculate IC50 value Message-Id: <-39413-090601153115-6386-95JepoXYlM8UaMVAoewMww!=!server.ccl.net> X-Original-From: Farhan Pasha Content-Type: multipart/alternative; boundary="0-998452351-1243884665=:87779" Date: Tue, 2 Jun 2009 01:01:05 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: Farhan Pasha [pashafa*yahoo.co.in] --0-998452351-1243884665=:87779 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hello I am not sure if there is any such software and what is authenticity of tha= t. It seems you are looking for some QSAR type tool, in that case there is = some possibilities but need efforts not just on mouse click. Well if you re= ally looking for QSAR please write in detail the exact need then i can do s= omething. Pasha Correspondence Address =0ADr. Syed Farhan Ahmad Pasha =0ARoom No. 5202 =0AInstitut de Biologie Structurale =0ALaboratoire de Dynamique Moleculaire =0A41 rue Jules Horowitz =0A38027 Grenoble cedex =0AFrance =0Atel : (+33) (0)4 38 78 99 28 =0Afax : (+33) (0)4 38 78 54 94 =0Afpasha],[rediffmail.com =0AURL:www.geocities.com/pashafa =0Awww.ibs.fr --- On Mon, 1/6/09, Kshatresh Dutta Dubey kshatresh++gmail.com wrote: > From: Kshatresh Dutta Dubey kshatresh++gmail.com Subject: CCL: Software to calculate IC50 value To: "Pasha, Frahan Ahmad " Date: Monday, 1 June, 2009, 5:02 PM Hi, Can anyone tell me about any =A0free software that calculates IC50 values f= rom binding energy or theoretical data?Any help will be heartly appreciated= .=0AThanks In advance.RegardsKshatresh Dutta Dubey=0A=0A=0A=0A Explore= and discover exciting holidays and getaways with Yahoo! India Travel http:= //in.travel.yahoo.com/ --0-998452351-1243884665=:87779 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Hello

I am not sure if there is any su= ch software and what is authenticity of that. It seems you are looking for = some QSAR type tool, in that case there is some possibilities but need effo= rts not just on mouse click. Well if you really looking for QSAR please wri= te in detail the exact need then i can do something.

Pasha

Co= rrespondence Address
=0ADr. Syed Farhan Ahmad Pasha
=0ARoom No. 5202<= br>=0AInstitut de Biologie Structurale
=0ALaboratoire de Dynamique Molec= ulaire
=0A41 rue Jules Horowitz
=0A38027 Grenoble cedex
=0AFrance<= br>=0Atel : (+33) (0)4 38 78 99 28
=0Afax : (+33) (0)4 38 78 54 94
= =0Afpasha],[rediffmail.com
=0AURL:www.geocities.com/pashafa
=0Awww.ibs.= fr

--- On Mon, 1/6/09, Kshatresh Dutta Dubey kshatresh++gmail.com= <owner-chemistry],[ccl.net> wrote:

From: Kshatresh Dutta Dubey kshatresh++gmail.com <owner-chemistr= y],[ccl.net>
Subject: CCL: Software to calculate IC50 value
To: "Pas= ha, Frahan Ahmad " <pashafa],[yahoo.co.in>
Date: Monday, 1 J= une, 2009, 5:02 PM

Hi,
<= /div>
Can anyone tell me about any  free software that calculates = IC50 values from binding energy or theoretical data?
A= ny help will be heartly appreciated.
=0A
Thanks In adva= nce.
Regards
Kshatresh Dutta Dube= y
=0A

=0A=0A=0A <= hr size=3D1> Bollywood news, movie reviews, film trailers and more! Click here. --0-998452351-1243884665=:87779-- From owner-chemistry@ccl.net Mon Jun 1 16:42:01 2009 From: "Bob Quandt rwquand**ilstu.edu" To: CCL Subject: CCL: Spartan 02 problems Message-Id: <-39414-090601152109-5233-jESpMT0ZB3KDTh5oF+Kefw ~ server.ccl.net> X-Original-From: "Bob Quandt" Date: Mon, 1 Jun 2009 15:21:05 -0400 Sent to CCL by: "Bob Quandt" [rwquand^_^ilstu.edu] All, We have Spartan 02 installed on several Linux boxes running SUSE 9. For security reasons we tried upgrading one machine to OpenSUSE 11.1 but encounter the error "/usr/local/spartan02.119a_22/sp_builderOPENGL: relocation error: /usr/local/spartan02.119a_22/sp_builderOPENGL: symbol errno, version GLIBC_2.0 not defined in file libc.so.6 with link time reference". It appears to be a problem with the updated glibc libraries (We got the same error with openSUSE 10). We have tried installing the old glibc 2.3.2 libraries in a separate directory and using the LD_ASSUME_KERNEL and LD_LIBRARY_PATH commands but then the shell (Bash and Csh) can't find their needed libraries. We even tried e-mailing Wavefunction INC. but they don't support Spartan 02 anymore and upgrading is cost prohibitive at this point. We can't be the first people to run into this problem. Has anyone out there run into this and/or come up with a solution? Any help would be greatly appreciated. Thank you in advance, Bob From owner-chemistry@ccl.net Mon Jun 1 19:00:00 2009 From: "Jonas Baltrusaitis jasius_1|,|yahoo.com" To: CCL Subject: CCL: VASP vs CASTEP Message-Id: <-39415-090601185910-29106-bZMeoVZlwuoNRB7XLCznmw||server.ccl.net> X-Original-From: "Jonas Baltrusaitis" Date: Mon, 1 Jun 2009 18:59:06 -0400 Sent to CCL by: "Jonas Baltrusaitis" [jasius_1++yahoo.com] Hi, I am not quite sure if this is an appropriate question, so if it isn't please disregard it (or contact me directly) as it's not intended to offend anybody. I am thinking of purchasing solid state modeling package and have to choose between CASTEP and VASP. I was going to ask which one would be more appropriate to optimize structures, calculate band structure and TDOS, PDOS and IR spectra and comfortably visualize all of that for some molecular crystals. Ease of use in setting up the input is needed as well. Additionally, some annealing would be appropriate. Any other benefits drawbacks (besides price) would be appreciated. thanks Jonas