From owner-chemistry@ccl.net Sat Oct 16 10:20:01 2010 From: "Iain Moal Iain.Moal*cancer.org.uk" To: CCL Subject: CCL: free software to measure RMSD and align proteins Message-Id: <-42964-101016095805-26702-rGpBYstNKShNqp4m6kf/3Q _ server.ccl.net> X-Original-From: Iain Moal Content-Language: en-GB Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Sat, 16 Oct 2010 14:54:51 +0100 MIME-Version: 1.0 Sent to CCL by: Iain Moal [Iain.Moal===cancer.org.uk] I find ProFit (http://www.bioinf.org.uk/software/profit/index.html) to be very good. I also occasionally use SAP or MUSTANG. There are many others available: http://en.wikipedia.org/wiki/Structural_alignment_software Iain M ________________________________________ > From: owner-chemistry+iain.moal==cancer.org.uk,ccl.net [owner-chemistry+iain.moal==cancer.org.uk,ccl.net] On Behalf Of Andrew Voronkov drugdesign%x%yandex.ru [owner-chemistry,ccl.net] Sent: 15 October 2010 16:14 To: Iain Moal Subject: CCL: free software to measure RMSD and align proteins Sent to CCL by: Andrew Voronkov [drugdesign/./yandex.ru] Dear CCL users, can you please recommend free software for homologic proteins comparison, alignment and RMSD measurements. I know DS visualizer and VMD, but is there anything else? Best regards, Andrewhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a registered charity in England and Wales (1089464) and in Scotland (SC041666) and a company limited by guarantee registered in England and Wales under number 4325234. Our registered address is Angel Building, 407 St John Street, London, EC1V 4AD. Our central telephone number is 020 7242 0200. This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so. From owner-chemistry@ccl.net Sat Oct 16 10:55:00 2010 From: "Guilherme Lu s Cordeiro guilhermecord(!)gmail.com" To: CCL Subject: CCL:G: Problem in SCIPCM Optimization Message-Id: <-42965-101016103114-28500-71pBc8waJF0SEQ7Ti0qHOg:server.ccl.net> X-Original-From: "Guilherme Lu s Cordeiro" Date: Sat, 16 Oct 2010 10:31:13 -0400 Sent to CCL by: "Guilherme Lu s Cordeiro" [guilhermecord#,#gmail.com] Dear CCL members, I am trying to perform a flavonoid optmization in ethanolic solution, but I got a problem while doing it. Part of my input data was as follows: %mem=6MW %nproc=1 %chk=QUER.ch ----------------------------------------- #T B3LYP/6-31G(d,p) SCRF(SCIPCM) Opt Test ----------------------------------------- -------------------- Quercetin in Ethanol -------------------- Symbolic Z-matrix: Charge = 0 Multiplicity = 1 The output shows the following error: Rotational constants (GHZ): 0.5907837 0.1401203 0.1132581 Isotopes: C-12,C-12,C-12,C-12,O-16,C-12,O-16,O-16,O-16,C-12,C-12,C-12,C-12,H-1,O -16,H-1,C-12,C-12,C-12,C-12,C-12,C-12,H-1,O-16,O-16,H-1,H-1,H-1,H-1,H-1,H-1,H-1 380 basis functions 686 primitive gaussians 78 alpha electrons 78 beta electrons nuclear repulsion energy 1690.1211869024 Hartrees. Projected INDO Guess. Integral accuracy reduced to 1.0D-05 until final iterations. WANTED AN INTEGER AS INPUT. FOUND A FLOATING POINT NUMBER AS INPUT. 1 2 1.5 6 1.5 8 1.0 ? Error termination via Lnk1e in C:\G98W\l502.exe. I would like any help. Thanks. From owner-chemistry@ccl.net Sat Oct 16 14:12:00 2010 From: "may abdelghani may01dz|yahoo.fr" To: CCL Subject: CCL: full electron basis sets for Re atom Message-Id: <-42966-101016135314-15947-WoKUWJBQMOd5BtJBRK0JtQ+/-server.ccl.net> X-Original-From: may abdelghani Content-Type: multipart/alternative; boundary="0-216652462-1287251584=:36866" Date: Sat, 16 Oct 2010 18:53:04 +0100 (BST) MIME-Version: 1.0 Sent to CCL by: may abdelghani [may01dz^_^yahoo.fr] --0-216652462-1287251584=:36866 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable =0A=0A=0A=0ADear CLL ers, I look for any Re(and Pt) full electron basis sets=A0; =0A=0A may abdelghani=09Laboratoire de chimie des mat=E9riaux et des vivants: Acti= vit=E9, R=E9activit=E9 =0A=0A=0A --0-216652462-1287251584=:36866 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
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Dear CLL ers,

I look for any Re(and Pt) f= ull electron basis sets ;

=0A=0A

may = abdelghani=09
= Laboratoire de chimie des mat=E9riaux et des vivants: Activit=E9, R= =E9activit=E9



=0A= =0A=0A=0A=0A --0-216652462-1287251584=:36866-- From owner-chemistry@ccl.net Sat Oct 16 14:47:00 2010 From: "Jan Labanowski janl(!)speakeasy.net" To: CCL Subject: CCL: Contract for documentation available from the InChI project Message-Id: <-42967-101016141000-4407-0+JoP4+mMH46tBI8hzVvvw+*+server.ccl.net> X-Original-From: Jan Labanowski Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="utf-8" Date: Sat, 16 Oct 2010 14:09:54 EDT MIME-Version: 1.0 Sent to CCL by: Jan Labanowski [janl(!)speakeasy.net] I was asked to post this announcement on CCL [Jan Labanowski] ------------------------------------------------------------ Under a contract from the InChI Trust ( http://www.inchi-trust.org ), Digital Chemistry has prepared a detailed report and specifications for high level documentation of the InChI algorithm and related software. The Trust now wishes to contract to undertake this documentation effort. The following provides the background/summary for the work. Details and the full RFP can be obtained from Steve Heller. Individuals and organizations are encouraged to submit bids for this work. The deadline for submission of bids is 12 November 2010. All responses to this RFP will be evaluated by a technical panel from the IUPAC Division VIII InChI subcommittee, the group responsible for the InChI standard. Steve Heller Project Director InChI Trust Summary: Though a substantial amount of documentation for users of InChIs and the InChI Software is available, detailed technical documentation of the algorithms used, and of the program code itself, is incomplete and somewhat scattered. Documentation is required both to rigorously describe the process of creating an InChI so that it can in principle be re-implemented de novo, and to describe the way in which that process is implemented in the existing InChI program code. To a considerable extent the current definition of the InChI-generation process is the existing program itself, and we therefore recommend that the appropriate sections of the existing Technical Manual be expanded to give full program documentation with references to the program code. Though the original code authors are likely to be able to produce appropriate documentation in the shortest time, an independent documentation writer is likely to be able to document it more comprehensively. We estimate that an independent writer would need around 20 days for the task. Steve Heller Project Director InChI Trust steve-,-inchi-trust.org From owner-chemistry@ccl.net Sat Oct 16 16:05:00 2010 From: "Kirk Peterson kipeters,,wsu.edu" To: CCL Subject: CCL: full electron basis sets for Re atom Message-Id: <-42968-101016160238-30815-VhNmGboHLN930wKmeW9Pfg]_[server.ccl.net> X-Original-From: Kirk Peterson Content-Type: multipart/alternative; boundary=Apple-Mail-4--285498319 Date: Sat, 16 Oct 2010 13:02:26 -0700 Mime-Version: 1.0 (Apple Message framework v1081) Sent to CCL by: Kirk Peterson [kipeters,wsu.edu] --Apple-Mail-4--285498319 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=iso-8859-1 Hi, Triple-zeta all-electron DK correlation consistent basis sets have been = published for the 5d metals in conjunction with pseudopotential based = ones in D. Figgen, K.A. Peterson, M. Dolg, and H. Stoll, J. Chem. Phys. = 130, 164108 (2009). These can be downloaded from = http://tyr0.chem.wsu.edu/~kipeters/basissets regards, Kirk ------------------------- Kirk A. Peterson Professor of Chemistry Department of Chemistry Washington State University Pullman, WA 99164-4630 office: (509) 335-7867 fax : (509) 335-8867 email: kipeters__wsu.edu web: http://tyr0.chem.wsu.edu/~kipeters/ On Oct 16, 2010, at 10:53 AM, may abdelghani may01dz|yahoo.fr wrote: > Dear CLL ers, >=20 > I look for any Re(and Pt) full electron basis sets ; >=20 >=20 >=20 > may abdelghani=09 > Laboratoire de chimie des mat=E9riaux et des vivants: Activit=E9, = R=E9activit=E9 >=20 >=20 >=20 --Apple-Mail-4--285498319 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=iso-8859-1 D. = Figgen, K.A. Peterson, M. Dolg, and H. Stoll, J. Chem. = Phys. 130, 164108 (2009).   These can be downloaded = > from http://tyr0.chem.wsu= .edu/~kipeters/basissets

regards,

Kirk

-------------------------

Kirk A. Peterson

Professor of = Chemistry

Washington State University

Pullman, WA = 99164-4630


office: (509) 335-7867

fax : (509) = 335-8867

kipeters__wsu.edu

web: http://tyr0.chem.wsu.edu/~kip= eters/




On Oct 16, 2010, at 10:53 AM, may abdelghani = may01dz|yahoo.fr wrote:

Dear CLL ers,

I look = for any Re(and Pt) full electron basis sets ;



may abdelghani =
Laboratoire de chimie des = mat=E9riaux et des vivants: Activit=E9, = R=E9activit=E9




= --Apple-Mail-4--285498319-- From owner-chemistry@ccl.net Sat Oct 16 17:24:00 2010 From: "Frank Neese neese*thch.uni-bonn.de" To: CCL Subject: CCL: full electron basis sets for Re atom Message-Id: <-42969-101016172253-30168-763Fwc+5a3NIk5Ahf+FWzQ++server.ccl.net> X-Original-From: Frank Neese Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Sat, 16 Oct 2010 23:22:26 +0200 Mime-Version: 1.0 (Apple Message framework v1081) Sent to CCL by: Frank Neese [neese(a)thch.uni-bonn.de] Hi, segmented all electron basis set for the first transition row and the lanthanides. Either with DKH or ZORA (non-relativistic calculations hardly make sense for those elements). Pantazis. D.; Neese, F. (2009) Construction and assessment of all-electron scalar relativistic basis sets for the lanthanides, J. Chem. Theor. Comp., 5, 2220-2238 Pantazis, D.; Chen, X.-Y.; Landis, C.R.; Neese, F. (2008) All Electron Scalar Relativistic Basis Sets for Third Row Transition Metal Atoms. J. Chem. Theor. Comp., 4, 908-919 in action and comparison to ECPs: Bühl, M.; Reimann, C.; Pantazis, D.A.; Bredow, T.; Neese, F. (2008) Geometries of Third-row Transition-Metal Complexes from Density-Functional Theory J. Chem. Theor. Comp., 4, 1449-1459 The basis sets are found in the supplement of the paper or are available via the ORCA program which is for free at: http://www.thch.uni-bonn.de/tc/orca/ All the best, Frank Neese