From owner-chemistry@ccl.net Mon Jun 23 06:35:01 2008 From: "andras.borosy*|*givaudan.com" To: CCL Subject: CCL: converting PQS output Message-Id: <-37230-080623063316-24891-nAxgjRwRFgqwAVWT8rYd0Q=-=server.ccl.net> X-Original-From: andras.borosy===givaudan.com Content-Type: multipart/alternative; boundary="=_alternative 0036EAA8C1257471_=" Date: Mon, 23 Jun 2008 11:59:41 +0200 MIME-Version: 1.0 Sent to CCL by: andras.borosy[-]givaudan.com This is a multipart message in MIME format. --=_alternative 0036EAA8C1257471_= Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable Unfortunatley not: n1 105% babel -ipqs NoCat.TSendo.tol.TS.out -omdl=20 NoCat.TSendo.tol.TS.out.mol=20 Segmentation fault I have: Open Babel 2.1.1 -- Dec 12 2007 -- 23:34:41 *|* Suse 9.2 Regards, Dr. Andr=E1s P=E9ter Borosy Scientific Modelling Expert Fragrance Research Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - D=FCbendorf -= =20 Switzerland T:+41-44-824 2164 - F:+41-44-8242926 - http://www.givaudan.com "Geoffrey Hutchison geoffh+.*|*.pitt.edu" =20 Sent by: owner-chemistry*|*ccl.net 20.06.2008 13:55 Please respond to "CCL Subscribers" To "Borosy, Andras " cc Subject CCL: converting PQS output Sent to CCL by: Geoffrey Hutchison [geoffh+*|*pitt.edu] > How can the optimised geometry be converted > from a PQS out or log file into a MDL mol file > (or any other standard file format like mol2, xyz, pdb)? This is exactly why Open Babel exists: http://openbabel.org/wiki/Parallel=5FQuantum=5FSolutions So you'd run: babel -ipqs -omdl Simply change to be whatever your PQS output is, and change as you wish. (Or pick "any other standard format.") Cheers, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geoffh,pitt.edu web: http://hutchison.chem.pitt.edu/ -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fmessagehttp://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fmessage Subscribe/Unsubscribe:=20 http://www.ccl.net/chemistry/sub=5Funsub.shtmlJob: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt--=_alternative 0036EAA8C1257471_= Content-Type: text/html; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable
Unfortunatley not:

n1 105% babel -ipqs  NoCat.TSe= ndo.tol.TS.out -omdl NoCat.TSendo.tol.TS.out.mol

Segmentation fault

I have:  Open Babel 2.1.1 -- Dec 12 2007 -- 23:34:41 *|* Suse 9.2

Regards,

Dr. Andr=E1s P=E9ter Borosy
Scientific Modelling Expert
Fragrance Research
Givaudan Schweiz AG  -  Ueberlandstrasse 138  -  CH-8600  -  D=FCbendorf  -  Switzerland
T:+41-44-824 2164  -  F:+41-44-8242926    -  http:= //www.givaudan.com


"Geoffrey Hutchi= son geoffh+.*|*.pitt.edu" <owner-chemistry*|*ccl.net>
Sent by: owner-chemistry*|*ccl.net

20.06.2008 13:55
Please respond to
"CCL Subscribers" <chemistry*|*ccl.net>
To
"Borosy, Andras " <andras.borosy*|*givaudan.com>
cc
Subject
CCL: converting PQS output





Sent to CCL by: Geoffrey Hutchison [geoffh+*|*pitt.edu]

> How can the optimised geometry be converted
> from a PQS out or log file into a MDL mol file
> (or any other standard file format like mol2, xyz, pdb)?

This is exactly why Open Babel exists:
http://openbabel.org/wiki/Parallel=5FQuantum=5FSolutions

So you'd run:
babel -ipqs <output file> -omdl <file.mdl>

Simply change <output file> to be whatever your PQS output is, and change
<file.mdl> as you wish. (Or pick "any other standard format.&quo= t;)

Cheers,
-Geoff

---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geoffh,pitt.edu
web: http://hutchison.chem.pitt.edu/



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--=_alternative 0036EAA8C1257471_=-- From owner-chemistry@ccl.net Mon Jun 23 07:52:01 2008 From: "Anthony Klon aklon++pcop.com" To: CCL Subject: CCL: Proton Affinities Message-Id: <-37231-080623074629-24506-11sWUjOLKIwfb47/2t4nGQ{=}server.ccl.net> X-Original-From: "Anthony Klon" Date: Mon, 23 Jun 2008 07:46:25 -0400 Sent to CCL by: "Anthony Klon" [aklon__pcop.com] Dear CCL, Could anyone give me guidance or point me in the right direction for references to calculate proton affinities using QM methods. In particular, the QM software I have available is GAMESS, so if there are any references for how to do this specifically with that software, it would be greatly appreciated. Sincerely, Anthony E. Klon Senior Scientist Molecular Modeling Pharmacopeia P.O. Box 5350 Princeton, NJ 08543-5350 609-452-3676 From owner-chemistry@ccl.net Mon Jun 23 09:46:01 2008 From: "Vincenzo Verdolino vincenzo.verdolino=-=nemo.unipr.it" To: CCL Subject: CCL: Proton Affinities Message-Id: <-37232-080623092056-8582-NdxvZKHcHP3M8VOgnxItog!=!server.ccl.net> X-Original-From: "Vincenzo Verdolino" Content-Type: text/plain; charset=iso-8859-1 Date: Mon, 23 Jun 2008 15:22:39 +0200 MIME-Version: 1.0 Sent to CCL by: "Vincenzo Verdolino" [vincenzo.verdolino(0)nemo.unipr.it] Dear take a look at J. Phys. Chem. A 2004, 108, 4485-4490 J. Am. Chem. Soc. 2000, 122, 6258-6262 J. Phys. Chem. A 2002, 106, 9947-9956 Thay are a good starting point If you need more about this, let me know Vincenzo Verdolino On Mon, 23 Jun 2008 07:46:25 -0400, Anthony Klon aklon++pcop.com wrote > Sent to CCL by: "Anthony Klon" [aklon__pcop.com] > Dear CCL, > > Could anyone give me guidance or point me in the right direction for > references to calculate proton affinities using QM methods. In > particular, the QM software I have available is GAMESS, so if there > are any references for how to do this specifically with that > software, it would be greatly appreciated. > > Sincerely, > > Anthony E. Klon > Senior Scientist > Molecular Modeling > Pharmacopeia > P.O. Box 5350 > Princeton, NJ 08543-5350 > 609-452-3676 > > -= 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> > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)-- Universita' degli Studi di Parma (http://www.unipr.it) From owner-chemistry@ccl.net Mon Jun 23 10:20:00 2008 From: "Steven Baker sdb034-#-latech.edu" To: CCL Subject: CCL: Molecular conductivity software Message-Id: <-37233-080622170741-16989-rSgtq134W79uLp9dwoP8Xw a server.ccl.net> X-Original-From: "Steven Baker" Date: Sun, 22 Jun 2008 17:07:38 -0400 Sent to CCL by: "Steven Baker" [sdb034+/-latech.edu] I am looking fr free software to model molecular conductivity and elecron transfer using TDDFT or Nonequilibrium Green Function Theory. Thanks From owner-chemistry@ccl.net Mon Jun 23 10:59:01 2008 From: "Balazs Jojart jojartb|a|pharm.u-szeged.hu" To: CCL Subject: CCL: DNA structure modification software Message-Id: <-37234-080619163632-7156-NoAsCqW8t55DWgUTMe1OYg[A]server.ccl.net> X-Original-From: Balazs Jojart Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-2; format=flowed Date: Thu, 19 Jun 2008 21:36:09 +0200 MIME-Version: 1.0 Sent to CCL by: Balazs Jojart [jojartb-$-pharm.u-szeged.hu] Hello Cesar, as far as I know, VMD is able to perform mutation. http://www.ks.uiuc.edu/Research/vmd/plugins/mutator/ hope this helps. balazs Cesar Millan pachequin[A]gmail.com írta: > 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 Mon Jun 23 11:31:01 2008 From: "John McKelvey jmmckel(!)gmail.com" To: CCL Subject: CCL: Core-Core Repulsions in ab initio and DFT methods Message-Id: <-37235-080623093300-11951-AThy60WwI5n4U+RjJCS5Kg.@.server.ccl.net> X-Original-From: "John McKelvey" Content-Type: multipart/alternative; boundary="----=_Part_22507_6781033.1214224398101" Date: Mon, 23 Jun 2008 08:33:18 -0400 MIME-Version: 1.0 Sent to CCL by: "John McKelvey" [jmmckel\a/gmail.com] ------=_Part_22507_6781033.1214224398101 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hello, Is there a discussion in the literature, other than for semi-empirical methods, about any circumstance wherein core-core interactions in ab initio [or DFT] should be other than ZaZb/Rab? Cheers! John McKelvey ------=_Part_22507_6781033.1214224398101 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hello,

Is there a discussion in the literature, other than for semi-empirical methods, about any circumstance wherein core-core interactions in ab initio [or DFT] should be other than ZaZb/Rab?

Cheers!

John McKelvey
------=_Part_22507_6781033.1214224398101-- From owner-chemistry@ccl.net Mon Jun 23 16:28:01 2008 From: "Ernst-Walter Knapp knapp+*+chemie.fu-berlin.de" To: CCL Subject: CCL: Proton Affinities Message-Id: <-37236-080623130036-22300-ewP6+t5sa4wd4z+6VdIvMg%%server.ccl.net> X-Original-From: Ernst-Walter Knapp Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Mon, 23 Jun 2008 18:06:40 +0200 MIME-Version: 1.0 Sent to CCL by: Ernst-Walter Knapp [knapp%%chemie.fu-berlin.de] Dear Anthony E. Klon, another useful reference for proton affinities and pKa computations is ChemPhysChem *5* (2004) 1513–1522 Sincerely, Walter Knapp -- |---------------------------------------------------------------------| | Dr. Ernst-Walter Knapp | | Free University of Berlin Tel.: +49 30 838 54387 | | Department of Biology, Chemistry, Pharmacy Fax.: +49 30 838 56921 | | Institute of Chemistry email: knapp:_:chemie.fu-berlin.de | | Macromolecular Modeling and Simulation of Biomolecular Systems | | Takustrasse 6 | | D-14195 Berlin | | Germany www: http://agknapp.chemie.fu-berlin.de | |---------------------------------------------------------------------| Vincenzo Verdolino vincenzo.verdolino=-=nemo.unipr.it wrote: >Sent to CCL by: "Vincenzo Verdolino" [vincenzo.verdolino(0)nemo.unipr.it] >Dear > >take a look at > J. Phys. Chem. A 2004, 108, 4485-4490 > J. Am. Chem. Soc. 2000, 122, 6258-6262 > J. Phys. Chem. A 2002, 106, 9947-9956 > >Thay are a good starting point > >If you need more about this, let me know > >Vincenzo Verdolino > >On Mon, 23 Jun 2008 07:46:25 -0400, Anthony Klon aklon++pcop.com wrote > > >>Sent to CCL by: "Anthony Klon" [aklon__pcop.com] >>Dear CCL, >> >>Could anyone give me guidance or point me in the right direction for >>references to calculate proton affinities using QM methods. In >>particular, the QM software I have available is GAMESS, so if there >>are any references for how to do this specifically with that >>software, it would be greatly appreciated. >> >>Sincerely, >> >>Anthony E. Klon >>Senior Scientist >>Molecular Modeling >>Pharmacopeia >>P.O. Box 5350 >>Princeton, NJ 08543-5350 >>609-452-3676 >> >>-= 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> >>Search Messages: http://www.ccl.net/htdig (login: ccl, Password: >>search)-- >> >> >Universita' degli Studi di Parma (http://www.unipr.it) > > > > > > > From owner-chemistry@ccl.net Mon Jun 23 17:04:01 2008 From: "Naseer MD mmdnaseer]|[gmail.com" To: CCL Subject: CCL: tool for rigid body - molecular movement Message-Id: <-37237-080623120047-791-6Aij6kS3+Y0QsxPWtbNYcg .. server.ccl.net> X-Original-From: "Naseer MD" Date: Mon, 23 Jun 2008 12:00:43 -0400 Sent to CCL by: "Naseer MD" [mmdnaseer,+,gmail.com] Dear colleagues, I am looking for a tool to perform rigid body movement of molecular plane(interms of pseudo bond length, bond angle and torsion angle). Can any one suggest me a tool to perform this task ? Many thanks. -naseer From owner-chemistry@ccl.net Mon Jun 23 17:38:02 2008 From: "Rafal Korlacki rkorlacki2[*]unl.edu" To: CCL Subject: CCL: converting PQS output Message-Id: <-37238-080623141151-11314-ukTunfjnm+qrDsvLwUZNXA~!~server.ccl.net> X-Original-From: "Rafal Korlacki" Content-Language: en-us Content-Type: multipart/alternative; boundary="----=_NextPart_000_0011_01C8D526.5723D9E0" Date: Mon, 23 Jun 2008 11:43:22 -0500 MIME-Version: 1.0 Sent to CCL by: "Rafal Korlacki" [rkorlacki2%%unl.edu] This is a multipart message in MIME format. ------=_NextPart_000_0011_01C8D526.5723D9E0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi, =20 If you cut the optimized geometry from PQS' log-file into an empty file, = and add a simple header: first line - number of atoms, second line - comment = or whatever, you will have a fully functional xyz file you can read and = convert using just any program. =20 Regards, =20 Rafal =20 =20 =20 =20 > From: owner-chemistry*_*ccl.net [mailto:owner-chemistry*_*ccl.net]=20 Sent: Friday, June 20, 2008 4:55 AM To: Korlacki, Rafal Subject: CCL: converting PQS output =20 Dear Colleagues,=20 How can the optimised geometry be converted > from a PQS out or log file into a MDL mol file (or any other standard file format like mol2, xyz, = pdb)? Regards,=20 Dr. Andr=E1s P=E9ter Borosy Scientific Modelling Expert Fragrance Research Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - D=FCbendorf = - Switzerland T:+41-44-824 2164 - F:+41-44-8242926 - http://www.givaudan.com ------=_NextPart_000_0011_01C8D526.5723D9E0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Hi,

 

If you cut the optimized geometry from PQS' = log-file into an empty file, and add a simple header: first line - number of atoms, = second line - comment or whatever, you will have a fully functional xyz file = you can read and convert using just any program.

 

Regards,

 

Rafal

 

 

 

 

From:= owner-chemistry*_*ccl.net [mailto:owner-chemistry*_*ccl.net]
Sent: Friday, June 20, 2008 4:55 AM
To: Korlacki, Rafal
Subject: CCL: converting PQS output

 


Dear Colleagues,

How = can the optimised geometry be converted > from a PQS out or log file into a = MDL mol file (or any other standard file format like mol2, xyz, pdb)? =

Regards,

Dr. = Andr=E1s P=E9ter Borosy
Scientific Modelling Expert
Fragrance Research
Givaudan Schweiz AG  -  Ueberlandstrasse 138  - =  CH-8600  -  D=FCbendorf  -  Switzerland
T:+41-44-824 2164  -  F:+41-44-8242926    -  http://www.givaudan.com

------=_NextPart_000_0011_01C8D526.5723D9E0-- From owner-chemistry@ccl.net Mon Jun 23 18:12:01 2008 From: "Geoffrey Hutchison geoffh+:_:pitt.edu" To: CCL Subject: CCL: converting PQS output Message-Id: <-37239-080623164146-2251-54OHvRb21vupUHAveBdydg^-^server.ccl.net> X-Original-From: Geoffrey Hutchison Content-transfer-encoding: 7bit Content-type: text/plain; delsp=yes; format=flowed; charset=US-ASCII Date: Mon, 23 Jun 2008 16:41:34 -0400 MIME-version: 1.0 (Apple Message framework v924) Sent to CCL by: Geoffrey Hutchison [geoffh+(0)pitt.edu] > Unfortunatley not: > n1 105% babel -ipqs NoCat.TSendo.tol.TS.out -omdl > NoCat.TSendo.tol.TS.out.mol I sent a reply this morning, but haven't seen it posted. I admit, I haven't used the PQS code in Open Babel -- it was contributed. But certainly it shouldn't be crashing. Please send me the file (or similar) and I will fix the bug. Considering Open Babel 2.2.0 is intended for release soon, I would like to take care of this ASAP. Thanks very much, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geoffh*pitt.edu web: http://hutchison.chem.pitt.edu/ From owner-chemistry@ccl.net Mon Jun 23 18:47:00 2008 From: "Kyle Beran beran_k=utpb.edu" To: CCL Subject: CCL: Proton Affinities Message-Id: <-37240-080623112603-6832-2Qergr/O4i9bYJNCuk4H3w]=[server.ccl.net> X-Original-From: "Kyle Beran" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 23 Jun 2008 09:52:22 -0500 MIME-Version: 1.0 Sent to CCL by: "Kyle Beran" [beran_k(-)utpb.edu] Anthony Check the following reference... Eur. J. Mass Spectr. 2006, 12, 385-396. Regards, Kyle -----Original Message----- > From: owner-chemistry]*[ccl.net [mailto:owner-chemistry]*[ccl.net] Sent: Monday, June 23, 2008 6:46 AM To: Beran, Kyle Subject: CCL: Proton Affinities Sent to CCL by: "Anthony Klon" [aklon__pcop.com] Dear CCL, Could anyone give me guidance or point me in the right direction for references to calculate proton affinities using QM methods. In particular, the QM software I have available is GAMESS, so if there are any references for how to do this specifically with that software, it would be greatly appreciated. Sincerely, Anthony E. Klon Senior Scientist Molecular Modeling Pharmacopeia P.O. Box 5350 Princeton, NJ 08543-5350 609-452-3676http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Mon Jun 23 21:24:01 2008 From: "Jozsef Csontos jozsefcsontos*|*creighton.edu" To: CCL Subject: CCL:G: g03: problem with link1 Message-Id: <-37241-080623211456-25009-MXttaBrSQBN0/JG4ts4VBg,,server.ccl.net> X-Original-From: Jozsef Csontos Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Mon, 23 Jun 2008 20:14:45 -0500 Mime-Version: 1.0 Sent to CCL by: Jozsef Csontos [jozsefcsontos---creighton.edu] If I can recall it correctly I had similar problem when I hadn't had the compatibility libraries installed. Try to list them, rpm -qa|grep compat and yum list available compat* If I'm right you should have a couple of c, c++, f77 and readline libraries installed. I hope it helps, Jozsef By the way, try to contact the gaussian support, if you haven't done yet. (Commercial representatives keep saying that how superior their product support...) On Sun, 2008-06-22 at 23:46 +0200, K.Radacki K.Radacki__mail.uni-wuerzburg.de wrote: > Vincenzo Verdolino vincenzo.verdolino=nemo.unipr.it wrote: > > Could you copy and paste the input and output file? Do you have this > > problem executing g03 as user or root? > > > I've tried both as normal user from group qchem (owner of > g03-directory) and as root. > > Input: > %MEM=100MB > %NPROC=2 > %CHK=BNH2 > %SAVE > > #P OPT=(Z-Matr,TIGHT) POP=FULL B3LYP/6-31G(D,P) > # SCF=(MAXCYCLE=150) INT=(GRID=99590) > > [=> B-NH2 > > 0 1 > X > B 1 c2 > N 2 r1 1 c90 > H 3 r2 2 a2 1 c90 > H 3 r2 2 a2 1 -c90 > > r1=1.3 > r2=.9 > a2=120. > > c2=2. > c90=90. > > > Output: > Entering Gaussian System, Link 0=g03 > Initial command: > /usr/local/SW/g03/l1.exe /tmp/Gau_8192/Gau-8203.inp > -scrdir=/tmp/Gau_8192/ > > and additionally the last line of /var/log/messages: > Jun 22 23:44:09 hall14 kernel: l1.exe[8204]: segfault at > 00000f85f11c48c0 rip 00000000004804ce rsp 0000007fbfffac80 error 4 > > The link l1.exe itself works and is generating following output: > PGFIO-F-211/OPEN/unit=5/invalid file name. > File name = stdin formatted, sequential access record = 0 > In source file l1init.f, at line number 141 > > Or if I try to start directly l1.exe BNH2.com I see ~normal~ output: > Default is to use a total of 2 processors: > 2 via shared-memory > 1 via Linda > Entering Link 1 = l1.exe PID= 8256. > ... > ... > ****************************************** > Gaussian 03: AM64L-G03RevD.01 13-Oct-2005 > 22-Jun-2008 > ****************************************** > %MEM=100MB > %NPROC=2 > Will use up to 2 processors via shared memory. > %CHK=BNH2 > %SAVE > Segmentation fault > > > In between I've updated CentOS to last available from repositories > kernel 2.6.9-34 -->>> 2.6.9-67.0.15 and observed no difference in > behavior. > I recompiled gaussian with standard blas in place of amcl all in vain. > > I have still an option to compile it with IFC but I never did it on > opterons. I'm not going to install suse. > > > > > > On Sun, 22 Jun 2008 12:15:01 +0200, K.Radacki > > K.Radacki(~)mail.uni-wuerzburg.de wrote > > > Sent to CCL by: "K.Radacki" [K.Radacki|*|mail.uni-wuerzburg.de] As > > already some people write to me with questions about > > user/group/world policies. > > > > > > The g03root is: > > > lrwxrwxrwx 1 root root 19 Jun 21 12:43 g03 -> > > g03.d1-acml40_64Int > > > drwxr-x--- 2 root qchem 12288 Jun 21 19:10 g03.d1-acml40_64Int > > > and all executable are > > > "-rwxr-x--- 1 root qchem" > > > > > > I fooled around a bit more and found out that probably for my > > trouble is responsible system. > > > I took the whole g03 directory > from machine where it was > > compiled (CentOS4.3) and I move it to different one (SUSE 9). > > > After copying PGI/.../lib and setting LD_LIBRARY_PATH the > > calculation were finished successfully. > > > > > > In /var/log/messages I found entry: > > > ... kernel: l1.exe[29525]: segfault at 00000f85f11c4920 rip > > 000000000048051e rsp 0000007fbfffab80 error 4 > > > I copied the binaries to another CentOS machine and observed the > > same result. > > > > > > The CentOS machine useing kernel 2.6.9-34.ELsmp and the SUSE: > > 2.6.5-7.244-smp (by the way all three machines have the same > > hardware) > > > > > > I would be very grateful for any clues > > > kristhe strange characters on the top line to the /a\ sign. You > > can alsoE-mail to subscribers: CHEMISTRY/a\ccl.net or use:http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtml> > > > > > -- > > Universita' degli Studi di Parma (http://www.unipr.it) > > > > > > > -- Jozsef Csontos, Ph.D. http://bif9.creighton.edu/csontos (jozsefcsontos_at_creighton_dot_edu) Department of Biomedical Sciences Creighton University, Omaha, NE From owner-chemistry@ccl.net Mon Jun 23 23:55:01 2008 From: "Son Won-joon onejune.son|a|gmail.com" To: CCL Subject: CCL: Molecular conductivity software Message-Id: <-37242-080623235116-31638-ui+blySKpQ3Q1biC0HaDcQ(!)server.ccl.net> X-Original-From: "Son Won-joon" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 24 Jun 2008 11:49:51 +0900 MIME-Version: 1.0 Sent to CCL by: "Son Won-joon" [onejune.son*gmail.com] Dear Steven Baker, Some of my friends are taking the advantage of Smeagol. You can download the code at http://www.smeagol.tcd.ie/, I hope :-) On 6/23/08, Steven Baker sdb034-#-latech.edu wrote: > > Sent to CCL by: "Steven Baker" [sdb034+/-latech.edu] > I am looking fr free software to model molecular conductivity and elecron transfer using TDDFT or Nonequilibrium Green Function Theory. Thanks> > > -- Son, Won-joon (-) Comp. Mat. Res. Lab Department of Physics Ewha Womans University Seoul, South Korea