From owner-chemistry@ccl.net Tue May 22 03:28:00 2007 From: "andrea spitaleri spitaleri.andrea%a%hsr.it" To: CCL Subject: CCL: HADDOCK installation Message-Id: <-34319-070522032645-16087-o5dLekg51a8hy2VhuJ3v4A|a|server.ccl.net> X-Original-From: andrea spitaleri Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 22 May 2007 09:26:17 +0200 MIME-Version: 1.0 Sent to CCL by: andrea spitaleri [spitaleri.andrea_._hsr.it] Hi, I am actually using HADDOCK and it quite easy to install it: 1. install python & cns 2. copy somewhere the haddock package 3. set the environment that's it! for more information, just have look to the HADDOCK mailing list Regards andrea Kalyan chaitanya kalyanpulipaka###gmail.com wrote: > Dear all, > > Is there any one who have worked with HADDOCK for protein-protein > docking, iam facing a challenge with installation of the same software.... > > Thanks in advance, > > P.Kalyan. -- ------------------------------- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom/ ------------------------------- ******************************************************************** Sostieni la ricerca del San Raffaele con il 5permille! E' SEMPLICE E NON COSTA NULLA. Basta indicare nell'apposito riquadro della dichiarazione dei redditi ("Ricerca sanitaria") il codice fiscale della Fondazione Centro S. Raffaele del Monte Tabor: 03 06 42 80 153 e ricordarsi di firmare. Se vuoi saperne di piu' scrivi a 5permille() hsr.it o vai sul sito www.5xmille.org From owner-chemistry@ccl.net Tue May 22 04:03:01 2007 From: "Jens Spanget-Larsen spanget||ruc.dk" To: CCL Subject: CCL: Vibrational structure of secondary amides in the solid state? Message-Id: <-34320-070522033120-17535-tvgWYgaXviiiv2ZuBR7q7g .. server.ccl.net> X-Original-From: Jens Spanget-Larsen Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 22 May 2007 09:30:47 +0200 MIME-Version: 1.0 Sent to CCL by: Jens Spanget-Larsen [spanget:ruc.dk] Dear CCL! Any experience with DFT or ab initio theoretical modeling of the vibrational structure of secondary amides in the crystalline state? Yours, Jens >--< ------------------------------------------------------ JENS SPANGET-LARSEN Office: +45 4674 2710 Dept. of Science (18.1) Fax: +45 4674 3011 Roskilde University Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget**ruc.dk DK-4000 Roskilde, Denmark http://www.ruc.dk/~spanget ------------------------------------------------------ From owner-chemistry@ccl.net Tue May 22 15:05:00 2007 From: "Hunter, Ken ken.hunter-$-uleth.ca" To: CCL Subject: CCL:G: locally dense basis sets and Inaccurate quadrature in CalDSu error Message-Id: <-34321-070522150306-21456-/QBFfeogjOYFFqGZE6w1cA:server.ccl.net> X-Original-From: "Hunter, Ken" Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C79CA3.C6FF6778" Date: Tue, 22 May 2007 13:02:43 -0600 MIME-Version: 1.0 Sent to CCL by: "Hunter, Ken" [ken.hunter]*[uleth.ca] This is a multi-part message in MIME format. ------_=_NextPart_001_01C79CA3.C6FF6778 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable I am trying to do a test calculation using locally dense basis sets (LDBS) on ethane, where different basis sets are split on each end of the double bond. I am using Gaussian 03, Revision D.02. When doing so I get the Inaccurate quadrature in CalDSu error when I use the following input: =20 # B3LYP/Gen =20 title =20 0 1 C 0.0 0.0 0.7 C 0.0 0.0 -.7 H 0.0 0.6 1.2 H 0.0 -.6 1.2 H 0.0 0.6 -1.2 H 0.0 -.6 -1.2 =20 1 3 4 0 3-21G **** 2 5 6 0 sto-3g **** =20 =20 Any assistance would be greatly appreciated. =20 Ken Hunter =20 =20 ------_=_NextPart_001_01C79CA3.C6FF6778 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

I am trying to do a = test calculation using locally dense basis sets (LDBS) on ethane, where = different basis sets are split on each end of the double bond. I am using = Gaussian 03, Revision D.02. When doing so I get the Inaccurate quadrature in = CalDSu error when I use the following input:

# = B3LYP/Gen

title

0 = 1

C = 0.0 0.0 0.7

C = 0.0 0.0 -.7

H = 0.0 0.6 1.2

H = 0.0 -.6 1.2

H = 0.0 0.6 -1.2

H = 0.0 -.6 -1.2

1 3 4 = 0

3-21G

****

2 5 6 = 0

sto-3g

****

Any assistance would be greatly = appreciated.

Ken Hunter

------_=_NextPart_001_01C79CA3.C6FF6778-- From owner-chemistry@ccl.net Tue May 22 17:11:00 2007 From: "Shobe, David David.Shobe ~~ sud-chemie.com" To: CCL Subject: CCL:G: locally dense basis sets and Inaccurate quadrature in CalDSu error Message-Id: <-34322-070522170751-20998-vIWXtALq11HKvK9kGOehSg],[server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C79CB5.2D7AF8DF" Date: Tue, 22 May 2007 23:07:15 +0200 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [David.Shobe{:}sud-chemie.com] This is a multi-part message in MIME format. ------_=_NextPart_001_01C79CB5.2D7AF8DF Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Just an offhand guess, but perhaps using the nosymm keyword would help? =20 After all, you're calculating a symmetric molecule with an asymmetric basis. =20 --David Shobe =20 =20 ________________________________ > From: owner-chemistry:ccl.net [mailto:owner-chemistry:ccl.net]=20 Sent: Tuesday, May 22, 2007 3:03 PM To: Shobe, David Subject: CCL:G: locally dense basis sets and Inaccurate quadrature in CalDSu error =20 I am trying to do a test calculation using locally dense basis sets (LDBS) on ethane, where different basis sets are split on each end of the double bond. I am using Gaussian 03, Revision D.02. When doing so I get the Inaccurate quadrature in CalDSu error when I use the following input: =20 # B3LYP/Gen =20 title =20 0 1 C 0.0 0.0 0.7 C 0.0 0.0 -.7 H 0.0 0.6 1.2 H 0.0 -.6 1.2 H 0.0 0.6 -1.2 H 0.0 -.6 -1.2 =20 1 3 4 0 3-21G **** 2 5 6 0 sto-3g **** =20 =20 Any assistance would be greatly appreciated. =20 Ken Hunter =20 =20 This e-mail message may contain confidential and / or privileged informatio= n. If you are not an addressee or otherwise authorized to receive this mess= age, you should not use, copy, disclose or take any action based on this e-= mail or any information contained in the message. If you have received this= material in error, please advise the sender immediately by reply e-mail an= d delete this message.=20 Thank you. ------_=_NextPart_001_01C79CB5.2D7AF8DF Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Just an offhand guess, but perhaps usi= ng the nosymm keyword would help?

After all, you’re calculating a symmetric molecule with an asymmetric basis.

--David Shobe=

From: owner-chemistry:ccl.net [mailto:owner-chemistry:ccl.net]
Sent: Tuesday, May 22, 2007 = 3:03 PM
To: Shobe, David
Subject: CCL:G: locally dense basis sets and Inaccurate quadrature in CalDSu error

I am trying to do a te= st calculation using locally dense basis sets (LDBS) on ethane, where differen= t basis sets are split on each end of the double bond. I am using Gaussian 03, Revision D.02. When doing so I get the Inaccurate quadrature in CalDSu error when I use the following input:

# B3LYP/Gen=

title

0 1<= /font>

C 0.0 0.0 0.7

C 0.0 0.0 -.7

H 0.0 0.6 1.2

H 0.0 -.6 1.2

H 0.0 0.6 -1.2

H 0.0 -.6 -1.2

1 3 4 0

3-21G

****=

2 5 6 0

sto-3g

****=

Any assistance would be greatly appreciated.

Ken Hunter

This e-mail message may contain confidential and / or privileged informatio= n. If you are not an addressee or otherwise authorized to receive this mess= age, you should not use, copy, disclose or take any action based on this e-= mail or any information contained in the message. If you have received this= material in error, please advise the sender immediately by reply e-mail an= d delete this message.
Thank you.

------_=_NextPart_001_01C79CB5.2D7AF8DF-- From owner-chemistry@ccl.net Tue May 22 17:55:01 2007 From: "Manali Joshi manali[#]adrik.bchs.uh.edu" To: CCL Subject: CCL: generate low resolution protein structure Message-Id: <-34323-070522175256-8216-F8MrUIawu1/bKScXRlizng a server.ccl.net> X-Original-From: "Manali Joshi" Date: Tue, 22 May 2007 17:52:53 -0400 Sent to CCL by: "Manali Joshi" [manali---adrik.bchs.uh.edu] Hello, I am looking for a software/tool that can take atomic coordinates from a protein pdb file and generate a low-resolution representation. Thanks in advance. -Manali From owner-chemistry@ccl.net Tue May 22 18:29:00 2007 From: "Andrew Orry andy{:}molsoft.com" To: CCL Subject: CCL: Workshop: Modern Drug Target Crystallography and Structure Based Drug Discovery Message-Id: <-34324-070522175848-12524-ntImomU58yqEQQY0n5nCkw++server.ccl.net> X-Original-From: Andrew Orry Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Tue, 22 May 2007 13:55:49 -0700 MIME-Version: 1.0 Sent to CCL by: Andrew Orry [andy-.-molsoft.com] Dear All, We still have a few places available at our two day workshop on the cutting-edge developments in crystallography and structure based drug design which will be held on June 28th-29th, 2007 in La Jolla California. 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 this rapidly advancing field. More information regarding registration and course content can be found here: http://www.ruppweb.org/workshops/Molsoft_workshop_2007.htm The course 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 includes protein crystallization demonstrations, actual structure determination using multiple anomalous dispersion methods and molecular replacement, model building and refinement, structure validation, analysis and interpretation, followed by in-silico ligand docking and virtual ligand screening. For more information please see: http://www.ruppweb.org/workshops/Molsoft_workshop_2007.htm E mail: andy^^^molsoft.com or call 858 625 2000 (x108). Thanks, Andy -- Andrew Orry Ph.D. Senior Scientist MolSoft LLC 3366 North Torrey Pines Court Suite 300 La Jolla, CA 92037 U S A Phone: (858) 625-2000 (x108) Fax: (858) 625-2888 www.molsoft.com From owner-chemistry@ccl.net Tue May 22 19:04:01 2007 From: "Elaine Meng meng#%#cgl.ucsf.edu" To: CCL Subject: CCL: generate low resolution protein structure Message-Id: <-34325-070522185640-14428-K03XzD2/GkJ5H38QI/cy0g---server.ccl.net> X-Original-From: "Elaine Meng" Date: Tue, 22 May 2007 18:56:36 -0400 Sent to CCL by: "Elaine Meng" [meng**cgl.ucsf.edu] Hi Manali, I don't know if this is what you had in mind, but given atomic coordinates of a protein, the Multiscale Models tool in Chimera will make a low-resolution surface. You can adjust the resolution in terms of how detailed the surface will be. Here is the man page: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemulti.html It can also build multimers, but it is not necessary for the structure to have higher-order symmetry. Chimera is free for academic/nonprofit use and can be downloaded from http://www.cgl.ucsf.edu/chimera Best, Elaine ----- Elaine C. Meng, Ph.D. meng-#-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 From owner-chemistry@ccl.net Tue May 22 20:04:00 2007 From: "Pratik Verma pratikv(-)stanford.edu" To: CCL Subject: CCL:G: error in g03 : Inv2 failed in DMIVCL Message-Id: <-34326-070522150802-22925-rcnfnP8Q9IyCn7cjmJ7ZKA|server.ccl.net> X-Original-From: "Pratik Verma" Date: Tue, 22 May 2007 15:07:57 -0400 Sent to CCL by: "Pratik Verma" [pratikv!^!stanford.edu] Hi all, Has anyone seen a solution for this error (highlighted by <<<<<<<<<<<) Warning! T( 1, 2)=0.95964990D+41 is big! T( 1, 1)=-.95964990D+41 T( 2, 2)=0.95964990D+41 Warning! T( 307, 227)=0.86473702D+01 is big! T( 307, 307)=0.84347148D+01 T( 227, 227)=0.78620756D+01 Warning! T( 227, 307)=0.94023729D+01 is big! T( 227, 227)=0.78620756D+01 T( 307, 307)=0.84347148D+01 Warning! T(1207,1570)=0.94625200D+02 is big! T(1207,1207)=0.47156731D+02 T(1570,1570)=0.18457225D+02 <<<<<<<<<<< Inv2 failed in DMIVCL. <<<<<<<<<<< Error termination via Lnk1e in /share/apps/g03/l502.exe at Sat May 19 17:21:06 2007. Job cpu time: 0 days 1 hours 21 minutes 44.9 seconds. File lengths (MBytes): RWF= 2160 Int= 0 D2E= 0 Chk= 13 Scr= 1 I am trying to do geometry optimizations and single point calculations using pcm and the UA0 and bondi atom type model. Odd thing is that only a few calculations out of many give this error even though all the input is the same for all. I have included the input below. %mem=7500MB %nproc=4 %chk=d3-fe3-ls-tmphen3-2z-b3l-sp-acn-bondi-300-3z.chk p uB3LYP/gen geom=check guess=read p iop(2/9=2) scfcyc=500 sp scrf=(pcm,solvent=acetonitrile,read) d3 phen fe(III) low spin 3 2 Fe N 0 6-311+g* **** C H 0 6-31g* **** radii=bondi tabs=300.0 nosymmcav tsare=0.1 pcmdoc Thanks,