From owner-chemistry@ccl.net Mon Jun 10 13:42:00 2013 From: "Elaine Meng meng a cgl.ucsf.edu" To: CCL Subject: CCL: new Chimera release (v1.8) Message-Id: <-48809-130610131932-23609-h+3USpL+GgVI80+c/v7q6Q(!)server.ccl.net> X-Original-From: "Elaine Meng" Date: Mon, 10 Jun 2013 13:19:30 -0400 Sent to CCL by: "Elaine Meng" [meng .. cgl.ucsf.edu] Hello everybody, A new production release of UCSF Chimera (version 1.8) is available: http://www.cgl.ucsf.edu/chimera/download.html Download is free for noncommercial use. Platforms: Windows, Mac, Linux, including 64-bit versions (recommended for working with large datasets on machines with at least 4GB memory). New features include a REST interface, session thumbnail images, electric field line display, interactive arrow repositioning, improvements to Animation, Mac multi-touch trackpad support, and suport for new formats: AutoPack results, Rich Molecular Format, Gromacs 4.6 trajectories, Amira mesh (scalar). More details are given below; see release notes for the full list: http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.8.html General: * new RESTServer tool (under Utilities) provides REST interface * text notes and thumbnail image can be saved along with a session, viewed in Restore Session file browser before opening a session * data items can be removed from the Rapid Access list * quit-Chimera confirmation default conditional instead of always * 2D Labels arrows can be repositioned interactively * Mac multi-touch trackpad support Structure Analysis and Modeling: * "connected fragment" inserted into selection cascade between residue and chain * H-bond and clash/contact detection can ignore intramolecular interactions * molecular surface parameters can be given in "surface" command * "split" command can split a model based on ligands, bonded sets of atoms, etc. (formerly just chains) * "~namesel" command to forget previously named selections * Autodock Vina tool checks for receptor and ligand hydrogens, adds them if missing (previously no hydrogens were added if the user chose not to add hydrogens with Chimera) * "pdb2pqr," "apbs," and "vina" command implementations of the respective graphical interfaces * support for Gromacs 4.6 trajectories (MD Movie tool) * RMF (Rich Molecular Format) Viewer for viewing hierarchical structural data and associated restraints from IMP (Integrative Modeling Platform, developed by the Sali group, UCSF) Animation enhancements and bugfixes: * "vseries" command implementation of Volume Series tool * "reset" command allows partially restoring a position * Animation mouse drag uses left mouse button instead of middle * Animation supports custom surface colorings * Animation works with volume isosurfaces Volume Data (Density Maps, ESP Maps): * "measure fieldLines" to display electric field lines for ESP maps * "measure mapStats" implementation of Volume Mean, SD, RMS tool * "vop threshold" to reassign values below a specified minimum and/or above a specified maximum * new input format Amira mesh (scalar) Enjoy! On behalf of the Chimera team, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco From owner-chemistry@ccl.net Mon Jun 10 14:48:01 2013 From: "Mathew D Halls mat.halls~~schrodinger.com" To: CCL Subject: CCL: Webinar: Simulations for Catalysis, Energy, and Nanotechnology 6-27-13 Message-Id: <-48810-130610144633-10905-vNSa7DCgudEa2QpaN1J7LQ*_*server.ccl.net> X-Original-From: "Mathew D Halls" Date: Mon, 10 Jun 2013 14:46:31 -0400 Sent to CCL by: "Mathew D Halls" [mat.halls^_^schrodinger.com] We are pleased to announce that the second materials science web seminar will be held June 27, 2013. This talk will be presented by Professor William A. Goddard III, the Charles and Mary Ferkel Professor of Chemistry and Director of the Materials and Process Simulation Center at the California Institute of Technology. The talk will illustrate the use of Schrodingers quantum chemistry package, Jaguar, in a range of applications. You are invited to register for this free presentation at the following link: http://contact.schrodinger.com/acton/ct/1250/s-021b-1306/Bct/l-028b/l- 028b:426/ct2_0/1 Best regards, Mathew D. Halls, Ph.D Director of Materials Science Schrodinger Inc. Office: (858) 643-9000 x201 mat.halls!=!schrodinger.com http://www.schrodinger.com From owner-chemistry@ccl.net Mon Jun 10 16:23:00 2013 From: "Silas Silva silas.silva]~[ufabc.edu.br" To: CCL Subject: CCL:G: Syntax error in Gaussian input file Message-Id: <-48811-130610143051-3505-FgBBO3pa2QpcLDeJyx47FA-.-server.ccl.net> X-Original-From: Silas Silva Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Mon, 10 Jun 2013 15:29:28 -0300 MIME-Version: 1.0 Sent to CCL by: Silas Silva [silas.silva#%#ufabc.edu.br] Hello all! I'm administrator of a supercomputing system. Much of our users run chemistry software. Recently, a user came up with a syntax error in her input file. This syntax error happens both in Gaussian 03 and Gaussian 09. Unfortunatelly, I couldn't help her, but I decided to come to this forum and ask experts. Below, I transcribe the error message and the whole input file. Can you please help me? Thanks! --- The error: QPErr --- A syntax error was detected in the input line. inglets,nstates=55) olyp/6-31g+(d) --- Part of the file: %chk=F_n2acc_1_td_va_BL %mem=46GB %nprocshared=8 #p td=(singlets,nstates=55) olyp/6-31g+(d) F_n2acc_1_td_va_BL -1 1 C -3.23822700 6.57445500 0.17417400 C -1.83011200 6.66437000 0.03801300 ... -- Silas Silva -- NTI - Computação Científica Universidade Federal do ABC +55 (11) 4437-8598 From owner-chemistry@ccl.net Mon Jun 10 17:16:00 2013 From: "kalyan onekalyan:-:yahoo.com" To: CCL Subject: CCL:G: Syntax error in Gaussian input file Message-Id: <-48812-130610165958-2476-fXiAtCTXmcEsuf3eAk9hyw---server.ccl.net> X-Original-From: kalyan Content-Type: multipart/alternative; boundary="_90220606-3CEE-0B6C-BAA8-F5A2D60608E4_" Date: Mon, 10 Jun 2013 22:59:50 +0200 MIME-Version: 1.0 Sent to CCL by: kalyan [onekalyan^yahoo.com] --_90220606-3CEE-0B6C-BAA8-F5A2D60608E4_ Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" I guess you forget to put space both in input line as well as end .=20 This is very common problems that we are doing . Best Regards=20 Kalyan -----Original Message----- > From: Silas Silva silas.silva]~[ufabc.edu.br Sent: 10/06/2013 22:45 To: Dhar, Kalyan kumar Subject: CCL:G: Syntax error in Gaussian input file Sent to CCL by: Silas Silva [silas.silva#%#ufabc.edu.br] Hello all! I'm administrator of a supercomputing system. Much of our users run chemistry software. Recently, a user came up with a syntax error in her input file. This syntax error happens both in Gaussian 03 and Gaussian 09. Unfortunatelly, I couldn't help her, but I decided to come to this forum and ask experts. Below, I transcribe the error message and the whole input file. Can you please help me? Thanks! --- The error: QPErr --- A syntax error was detected in the input line. inglets,nstates=3D55) olyp/6-31g+(d) --- Part of the file: %chk=3DF_n2acc_1_td_va_BL %mem=3D46GB %nprocshared=3D8 #p td=3D(singlets,nstates=3D55) olyp/6-31g+(d) F_n2acc_1_td_va_BL -1 1 C -3.23822700 6.57445500 0.17417400 C -1.83011200 6.66437000 0.03801300 ... --=20 Silas Silva -- NTI - Computa=E7=E3o Cient=EDfica Universidade Federal do ABC +55 (11) 4437-8598 -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt--_90220606-3CEE-0B6C-BAA8-F5A2D60608E4_ Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset="iso-8859-1"
I guess you forget to put space both in input line a= s well as end .

This is very common problems that we are doing .
Best Regards
Kalyan
From: Silas Silva sil= as.silva]~[ufabc.edu.br
Sent: 10/06/2013 22:45
To: Dhar, Kalyan kumar
Subject: CCL:G: Syntax = error in Gaussian input file


Sent to CCL by: Silas Silva = [silas.silva#%#ufabc.edu.br]
Hello all!

I'm administrator of a su= percomputing system.  Much of our users run
chemistry software.
=
Recently, a user came up with a syntax error in her input file.  T= his
syntax error happens both in Gaussian 03 and Gaussian 09.
Unfortu= natelly, I couldn't help her, but I decided to come to this
forum and as= k experts.  Below, I transcribe the error message and the
whole inp= ut file.

Can you please help me?

Thanks!

---

Th= e error:

QPErr --- A syntax error was detected in the input line.
inglets,nstates=3D55) olyp/6-31g+(d)

---

Part of the f= ile:

%chk=3DF_n2acc_1_td_va_BL
%mem=3D46GB
%nprocshared=3D8#p td=3D(singlets,nstates=3D55) olyp/6-31g+(d)

F_n2acc_1_td_va_BL
-1 1
C          = ;       -3.23822700    6.57445= 500    0.17417400
C      &= nbsp;          -1.83011200&nbs= p;   6.66437000    0.03801300

...

-= -
Silas Silva -- NTI - Computa=E7=E3o Cient=EDfica
Universidade Fede= ral do ABC
+55 (11) 4437-8598



-=3D This is automatically = added to each message by the mailing script =3D-
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= --_90220606-3CEE-0B6C-BAA8-F5A2D60608E4_-- From owner-chemistry@ccl.net Mon Jun 10 18:21:00 2013 From: "Herbert Fruchtl herbert.fruchtl:st-andrews.ac.uk" To: CCL Subject: CCL:G: Syntax error in Gaussian input file Message-Id: <-48813-130610181810-14297-zxcczLYp0krpCIk8gIodMg%server.ccl.net> X-Original-From: Herbert Fruchtl Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 10 Jun 2013 23:17:31 +0100 MIME-Version: 1.0 Sent to CCL by: Herbert Fruchtl [herbert.fruchtl,+,st-andrews.ac.uk] There's a typo in the basis set. It should be 6-31+g(d), not 6-31g+(d). HTH, Herbert On 10/06/13 19:29, Silas Silva silas.silva]~[ufabc.edu.br wrote: > > Sent to CCL by: Silas Silva [silas.silva#%#ufabc.edu.br] > Hello all! > > I'm administrator of a supercomputing system. Much of our users run > chemistry software. > > Recently, a user came up with a syntax error in her input file. This > syntax error happens both in Gaussian 03 and Gaussian 09. > Unfortunatelly, I couldn't help her, but I decided to come to this > forum and ask experts. Below, I transcribe the error message and the > whole input file. > > Can you please help me? > > Thanks! > > --- > > The error: > > QPErr --- A syntax error was detected in the input line. > > inglets,nstates=55) olyp/6-31g+(d) > > --- > > Part of the file: > > %chk=F_n2acc_1_td_va_BL > %mem=46GB > %nprocshared=8 > #p td=(singlets,nstates=55) olyp/6-31g+(d) > > F_n2acc_1_td_va_BL > > -1 1 > C -3.23822700 6.57445500 0.17417400 > C -1.83011200 6.66437000 0.03801300 > > ... > -- Herbert Fruchtl Senior Scientific Computing Officer School of Chemistry, School of Mathematics and Statistics University of St Andrews -- The University of St Andrews is a charity registered in Scotland: No SC013532