From owner-chemistry@ccl.net Mon Apr 23 03:56:00 2012 From: "steinbrt^rci.rutgers.edu" To: CCL Subject: CCL: Good site for finding books ( Search and Download directly) Message-Id: <-46757-120423035437-12657-65ssfyq1rOmbiW1KQQZ0oQ###server.ccl.net> X-Original-From: steinbrt:-:rci.rutgers.edu Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Mon, 23 Apr 2012 03:54:30 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: steinbrt(!)rci.rutgers.edu Hi all, I hope not to start another flame war on copyright vs. fair use/free speech, but the immediate threat of legal action for posting a link is a bit much in my opinion. While pointing out this site is certainly not ethical (and most likely against CCLs usage terms) I can not believe that it is illegal. Now OTOH downloading from such a site is certainly illegal, at least in my country, but as for hosting it, we have to accept that U.S. copyright laws do not necessarily apply in the Kingdom of Tonga. Kind Regards, Dr. Thomas Steinbrecher formerly at the BioMaps Institute Rutgers University 610 Taylor Rd. Piscataway, NJ 08854 From owner-chemistry@ccl.net Mon Apr 23 07:43:00 2012 From: "Herbert Fruchtl herbert.fruchtl*st-andrews.ac.uk" To: CCL Subject: CCL: Good site for finding books ( Search and Download directly) Message-Id: <-46758-120423050453-25510-YAdytCI983/r/Rr7y42Rzw.@.server.ccl.net> X-Original-From: Herbert Fruchtl Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 23 Apr 2012 10:04:39 +0100 MIME-Version: 1.0 Sent to CCL by: Herbert Fruchtl [herbert.fruchtl..st-andrews.ac.uk] Well, I also don't want a flame war, but you started it :-). I don't know the laws of the Kingdom of Tonga (I assume it has signed most of the usual international agreements), but CCL is hosted in the USA, and may be open to litigation. The sad fact is that you don't have to be in actual breach of the law. Having a bunch of corporate lawyers going after you may put somebody like Jan out of business long before anything reaches court. I quite like CCL and would like to keep it! Herbert On 23/04/12 08:54, steinbrt^rci.rutgers.edu wrote: > > Sent to CCL by: steinbrt(!)rci.rutgers.edu > Hi all, > > I hope not to start another flame war on copyright vs. fair use/free > speech, but the immediate threat of legal action for posting a link is a > bit much in my opinion. While pointing out this site is certainly not > ethical (and most likely against CCLs usage terms) I can not believe that > it is illegal. > > Now OTOH downloading from such a site is certainly illegal, at least in my > country, but as for hosting it, we have to accept that U.S. copyright laws > do not necessarily apply in the Kingdom of Tonga. > > Kind Regards, > > Dr. Thomas Steinbrecher > formerly at the > BioMaps Institute > Rutgers University > 610 Taylor Rd. > Piscataway, NJ 08854> > -- 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 From owner-chemistry@ccl.net Mon Apr 23 08:18:00 2012 From: "Robert A Lewis R.A.Lewis###hull.ac.uk" To: CCL Subject: CCL: Gaussview dipole moments Message-Id: <-46759-120423061657-10987-AqXsASVNa7c8qn4qxCM+Yw#server.ccl.net> X-Original-From: "Robert A Lewis" Content-Type: multipart/mixed; boundary="MIRAPOINT_PART1_4f952c12" Date: Mon, 23 Apr 2012 11:16:39 +0100 MIME-Version: 1.0 Sent to CCL by: "Robert A Lewis" [R.A.Lewis|*|hull.ac.uk] This is a multi-part message in MIME format. --MIRAPOINT_PART1_4f952c12 Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01CD213A.2CAB0617" ------_=_NextPart_001_01CD213A.2CAB0617 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable I am running Gaussview 5.0 with Guassian 09W. The output from charge calculations gives the net dipole moment and a graphical output but not the x,y, and z components. How can this information be obtained? =20 Regards =20 =20 Rob Lewis =20 =20 =20 Dr Robert A. Lewis Department of Chemistry University of Hull Cottingham Road Hull HU6 7RX T +44 (0)1482 466649 F +44(0)1482 466410 email: R.A.Lewis!^!hull.ac.uk =20 ------_=_NextPart_001_01CD213A.2CAB0617 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

I am = running Gaussview 5.0 with Guassian 09W. The output from charge = calculations gives the net dipole moment and a graphical output but not = the x,y, and z components. How can this information be = obtained?

 

Regards

 

 

Rob = Lewis

 

 

 

Dr Robert A. = Lewis

Department of = Chemistry

University of = Hull

Cottingham Road

Hull  HU6 7RX

T +44 (0)1482 466649

F +44(0)1482 466410

email: R.A.Lewis!^!hull.ac.uk

 

------_=_NextPart_001_01CD213A.2CAB0617-- --MIRAPOINT_PART1_4f952c12 Content-Disposition: inline Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit ************************************************** To view the terms under which this email is distributed, please go to http://www2.hull.ac.uk/legal/disclaimer.aspx ************************************************** --MIRAPOINT_PART1_4f952c12-- From owner-chemistry@ccl.net Mon Apr 23 08:55:00 2012 From: "steinbrt]|[rci.rutgers.edu" To: CCL Subject: CCL: Good site for finding books ( Search and Download directly) Message-Id: <-46760-120423084615-12139-sZ/TZLOmlwyZ9FwZObvHPQ!^!server.ccl.net> X-Original-From: steinbrt(-)rci.rutgers.edu Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Mon, 23 Apr 2012 08:46:08 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: steinbrt=-=rci.rutgers.edu Hi, I can't believe that I just read the Tongese Royal Copyright Act of 2002, but it seems to allow people to make a single private copy of any literary work for non-commercial use. That may not cover this website and is a moot point anyway, since 99.9% of users will download from elsewhere in the world where this is not allowed. > Well, I also don't want a flame war, but you started it :-). To further defuel the flames, I agree to what you said and CCL is no place for such posts which, legal or not, carry a danger to the site owner. Thomas Dr. Thomas Steinbrecher formerly at the BioMaps Institute Rutgers University 610 Taylor Rd. Piscataway, NJ 08854 From owner-chemistry@ccl.net Mon Apr 23 10:03:00 2012 From: "Andrew Voronkov drugdesign++yandex.ru" To: CCL Subject: CCL: free software for calculation of TPSA or PSA for ligands databases Message-Id: <-46761-120423080200-21235-VbpTwCKsLUDflnEjpc8CtA]![server.ccl.net> X-Original-From: Andrew Voronkov Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Mon, 23 Apr 2012 16:01:46 +0400 MIME-Version: 1.0 Sent to CCL by: Andrew Voronkov [drugdesign[-]yandex.ru] Dear CCL users, can anyone recommend free software for TPSA calculation where I can load database of ligands, for example several hundreds and ideally get the ranked according PSA. I am using now free Molinspiration server, but there is no file upload option, onl one by one option. Best regards, Andrew From owner-chemistry@ccl.net Mon Apr 23 10:38:00 2012 From: "Jan Labanowski janl#,#speakeasy.net" To: CCL Subject: CCL: Good site for finding books ( Search and Download directly) Message-Id: <-46762-120423103559-26666-xiFyMKCToXs3CUpOIXFcjg- -server.ccl.net> X-Original-From: Jan Labanowski Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="utf-8" Date: Mon, 23 Apr 2012 10:35:51 EDT MIME-Version: 1.0 Sent to CCL by: Jan Labanowski [janl+/-speakeasy.net] How this looks from the point of view of CCL maintainer... I do not censor the list. Apart from the fact that I consider it questionable, it would expose me to serious legal liabilities. As long as the CCL is a "phone company" and I do not control what people are chatting about, I am not responsible (at least this is my understanding). However, this does not mean that I will not be sued or some guys in leather trenches will not visit me (yes, the "munition software" and participants from the "axis of evil" countries). The method of destroying someone, in full glory of the law, by dragging him/her through the courts until they ran out of money for lawyers, is not new and dates to ancient Greece. It seems that it is put to "good" use more often today than it has been in the past. Look at "software patents" and "copyright infringements" for example. So please be responsible, since what you post to CCL will be posted. Of course, you can create "The CCL Legal Defense Fund" foundation with a war chest of 10 million dollars (but I know that CCL is not worth that much...). But even then, with the paid up slick Boston or LA lawyers on my side, I am not sure, I would go through the ordeal of wasting my life in the courts. Jan -- Jan Labanowski CCL Maintainer From owner-chemistry@ccl.net Mon Apr 23 11:12:00 2012 From: "Laurence Cuffe cuffe(_)mac.com" To: CCL Subject: CCL: Good site for finding books ( Search and Download directly) Message-Id: <-46763-120423080018-12660-S0Q0gtxjlMblD+VxjYsRZQ-*-server.ccl.net> X-Original-From: Laurence Cuffe Content-type: multipart/alternative; boundary="Boundary_(ID_WCgrO6/BLopmWmCEfUlRHg)" Date: Mon, 23 Apr 2012 11:58:43 +0000 (UTC) MIME-version: 1.0 Sent to CCL by: Laurence Cuffe [cuffe- -mac.com] --Boundary_(ID_WCgrO6/BLopmWmCEfUlRHg) Content-type: text/plain; charset=windows-1252; format=flowed Content-transfer-encoding: quoted-printable On Apr 22, 2012, at 03:57 PM, "Wolf Ihlenfeldt wdi]_[xemistry.com" wrote: Sent to CCL by: Wolf Ihlenfeldt [wdi.]-[.xemistry.com] Are you out of your mind to advertise for such a site on this forum? The Wiley title Fluid Mechanics, Heat Transfer, and Mass Transfer: Chemical Engineering Pr= actice easily found in the 'last added' section was only published April 12th, 2011 and retails on Amazon.com for USD 125. This is most definitely not a text in the public domain. My guess is that Wiley's lawyers will be most interested in your post and potential association with that site.... =20 This topic has come up before, and its worth noting that the list owner un= der "safe harbour rules" is in an invidious position with respect to posts= like this, as exerting strong editorial control can imply that the list o= wner is responsible for content. This is a legal situation which is very c= ountry dependent. On the larger question of whether putting the text above= online is legal, the answer is clearly a resounding no in most jurisdicti= ons. However, it is also worth noting that in some places, such action may= be legal, and that therefore the correspondent may not be doing anything = illegal in passing on the link to us, even though in most countries again = use of the service would be a violation of copyright, and an illegal act o= n our part.=20 =20 If you think the legal situation is complex, the moral situation is even m= ore so due to varying cultural norms, however If I was an author of one of= the texts mentioned, and I had not sanctioned this distribution channel, = I think I would be vey correctly annoyed, and it might lead to me stereoty= ping the poster, and other groups of which they might be a member in a way= which reflected poorly on them as a whole. In this context, its probabl= y worth considering the effect of such a post, before sending it to an int= ernational audience. =20 All the best Dr Laurence Cuffe.=20 On Sun, Apr 22, 2012 at 7:50 PM, Prashant Singh Rana psrana[-]gmail.com wrote: > > Good site for finding books ( Search and Download directly) > > http://free-books.us.to/ > > > -- > Thanks & Regards > > Prashant Singh Rana > PhD Research Scholar > Department of Information & Communication Technology > ABV-Indian Institute of Information Technology & Management (IIITM), Gwa= lior, MP, India. > > Contact: +91-9098236997 > +91-9313889932 > Email : psrana|,|iiitm.ac.in > psrana|,|gmail.com > > "Try to Fail, BUT Don't Fail to Try" -- Wolf-D. Ihlenfeldt - Xemistry GmbH - wdi]~[xemistry.com Phone: +49 6174 201455 - Fax +49 6174 209665 --- xemistry gmbh =96 Gesch=E4ftsf=FChrer/Managing Director: Dr. W. D. Ihlenfe= ldt Address: Hainholzweg 11, D-61462 K=F6nigstein, Germany HR K=F6nigstein B7522 : Ust/VAT ID DE215316329 : DUNS 34-400-1719 -=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= --Boundary_(ID_WCgrO6/BLopmWmCEfUlRHg) Content-type: multipart/related; boundary="Boundary_(ID_lsmk5fh+NhE+tvUmKVHMWQ)"; type="text/html" --Boundary_(ID_lsmk5fh+NhE+tvUmKVHMWQ) Content-type: text/html; charset=windows-1252 Content-transfer-encoding: quoted-printable


On Apr 22, 2012, at 03:57 PM, "Wolf Ihlenfeldt wdi]_[xemistry= com" <owner-chemistry]-[ccl.net> wrote:


Sent to CCL by: Wolf Ihlenfeldt [wdi.]-[.xemistry.= com]
Are you out of your mind to advertise for such a site on this foru= m?

The Wiley title

Fluid Mechanics, Heat Transfer, and Mass = Transfer: Chemical Engineering Practice

easily found in the 'last a= dded' section was only published April
12th, 2011 and retails on Amazon.com fo= r USD 125. This is most
definitely not a text in the public domain.
=
My guess is that Wiley's lawyers will be most interested in your post<= BR>and potential association with that site....

 

This t= opic has come up before, and its worth noting that the list owner under "s= afe harbour rules" is in an invidious position with respect to posts like = this, as exerting strong editorial control can imply that the list owner i= s responsible for content. This is a legal situation which is very country= dependent. On the larger question of whether putting the text above onlin= e is legal, the answer is clearly a resounding no in most jurisdictions. H= owever, it is also worth noting that in some places, such action may be le= gal, and that therefore the correspondent may not be doing anything illega= l in passing on the link to us, even though in most countries again use of= the service would be a violation of copyright, and an illegal act on our = part.

 

If you think the legal situation is complex, the moral situation i= s even more so due to varying cultural norms, however If I was an author o= f one of the texts mentioned, and I had not sanctioned this distribution c= hannel, I think I would be vey correctly annoyed, and it might lead to me = stereotyping the poster, and other groups of which they might be a member = in a way which reflected poorly on them as a whole.   In this context, its probably worth conside= ring the effect of such a post, before sending it to an international audi= ence.

 

All the best

Dr Laurence Cuffe.




On Sun, Apr 22, 2012 at 7:50 PM, Prashan= t Singh Rana
psrana[-]gmail.com <owner-chemistry]~[ccl.net> wrote= :
>
> Good site for finding books ( Search and Download direct= ly)
>
> http://free-books.us.to/
>
>
>= --
> Thanks & Regards
>
> Prashant Singh Rana
&g= t; PhD Research Scholar
> Department of Information & Communicat= ion Technology
> ABV-Indian Institute of Information Technology &= ; Management (IIITM), Gwalior, MP, India.
>
> Contact:  += 91-9098236997
>              &nbs= p; +91-9313889932
> Email   :   psrana|,|iiitm.a= c.in
>                 psran= a|,|gmail.com
>
> "Try to Fail, BUT Don't Fail to Try"

=


--
Wolf-D. Ihlenfeldt -  Xemistry GmbH - wdi]~[xemistr= y.com
Phone: +49 6174 201455 - Fax +49 6174 209665
---
xemistry g= mbh =96 Gesch=E4ftsf=FChrer/Managing Director: Dr. W. D. Ihlenfeldt
Add= ress: Hainholzweg 11, D-61462 K=F6nigstein, Germany
HR K=F6nigstein B75= 22 : Ust/VAT ID DE215316329 : DUNS 34-400-1719



-=3D This is= automatically added to each message by the mailing script =3D-
To reco= ver the email address of the author of the message, please change
the s= trange characters on the top line to the ]-[ sign. You can also
look up t= he X-Original-From: line in the mail header.

E-mail to subscribers:= CHEMISTRY]-[ccl.net or use:
http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mai= l to administrators: CHEMISTRY-REQUEST]-[ccl.net or us= e
http://www.ccl.net/cg= i-bin/ccl/send_ccl_message
http://www.ccl.net/chemistry/sub_unsub.sht= ml

Before posting, check wait time at: http://www.ccl.net

Job= : http://www.ccl.net/jobs
Conferences: http://server.ccl.net/chemistry= /announcements/conferences/

Search Messages: http://www.ccl.net/chemistry/searchccl= /index.shtml

If your mail bounces from CCL with 5.7.1 error, ch= eck:
http://www.ccl.net/spammers.txt

RTFI: <= A href=3D"http://www.ccl.net/chemistry/aboutccl/instructions/" _mce_href=3D= "http://www.ccl.net/chemistry/aboutccl/instructions/">http://www.ccl.net/c= hemistry/aboutccl/instructions/


= --Boundary_(ID_lsmk5fh+NhE+tvUmKVHMWQ)-- --Boundary_(ID_WCgrO6/BLopmWmCEfUlRHg)-- From owner-chemistry@ccl.net Mon Apr 23 11:47:00 2012 From: "Shirin Harisy ens2007-,-gmail.com" To: CCL Subject: CCL: How to restart a frequency using checkpoint file. Message-Id: <-46764-120423104531-14828-paY6gcVysXxAI8wHTs2ZNw(~)server.ccl.net> X-Original-From: "Shirin Harisy" Date: Mon, 23 Apr 2012 10:45:29 -0400 Sent to CCL by: "Shirin Harisy" [ens2007##gmail.com] the route section was #B3LYP/6-31G(d) freq optcyc=400 how can i restart this job thanks From owner-chemistry@ccl.net Mon Apr 23 12:22:00 2012 From: "Geoffrey Hutchison geoffh*pitt.edu" To: CCL Subject: CCL: free software for calculation of TPSA or PSA for ligands databases Message-Id: <-46765-120423113236-32263-oo/cNVLkdzZ3+C2kWHmYRw-$-server.ccl.net> X-Original-From: Geoffrey Hutchison Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=us-ascii Date: Mon, 23 Apr 2012 11:32:29 -0400 MIME-version: 1.0 (Apple Message framework v1257) Sent to CCL by: Geoffrey Hutchison [geoffh a pitt.edu] > Dear CCL users, can anyone recommend free software for TPSA calculation where I can load database of ligands, for example several hundreds and ideally get the ranked according PSA. I am using now free Molinspiration server, but there is no file upload option, onl one by one option. Best regards, Andrew There are undoubtedly multiple programs can do this, but this can be done simply with Open Babel: % Output as SMILES, sorted by TPSA and append the TPSA value to the title obabel ~/data/drugbank-ca.sdf --append TPSA --sort TPSA -O ~/data/db-sorted.smi % Or sort by TPSA, but add a SDF property field with the TPSA value obabel ~/data/drugbank-ca.sdf --sort TPSA --add TPSA -O ~/data/db-sorted.sdf Of course you can get it at http://openbabel.org/ Hope that helps, -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 Apr 23 12:57:00 2012 From: "Tapas Kar tapas.kar^^^usu.edu" To: CCL Subject: CCL: How to restart a frequency using checkpoint file. Message-Id: <-46766-120423124243-12183-1OLO537VB69B229JtoiftA-#-server.ccl.net> X-Original-From: Tapas Kar Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 23 Apr 2012 16:42:30 +0000 MIME-Version: 1.0 Sent to CCL by: Tapas Kar [tapas.kar]![usu.edu] Hello You have to use rwf file to restart freq job: Input example: %rwf=pathname/filename.rwf %chk= pathname/filename.chk %mem= #restart Good luck Tapas -----Original Message----- > From: owner-chemistry+tapas.kar==usu.edu_-_ccl.net [mailto:owner-chemistry+tapas.kar==usu.edu_-_ccl.net] On Behalf Of Shirin Harisy ens2007-,-gmail.com Sent: Monday, April 23, 2012 8:45 AM To: Tapas Kar Subject: CCL: How to restart a frequency using checkpoint file. Sent to CCL by: "Shirin Harisy" [ens2007##gmail.com] the route section was #B3LYP/6-31G(d) freq optcyc=400 how can i restart this job thankshttp://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 Apr 23 13:45:00 2012 From: "George Fitzgerald George.Fitzgerald#,#accelrys.com" To: CCL Subject: CCL: Good site for finding books ( Search and Download directly) Message-Id: <-46767-120423133603-19019-Gg8xW40bhMdebL2AiQ5nfg[a]server.ccl.net> X-Original-From: George Fitzgerald Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_55AC410F3302E740AC9EC50011F73E8F041AB9299CEXCH1COLOacce_" Date: Mon, 23 Apr 2012 10:35:49 -0700 MIME-Version: 1.0 Sent to CCL by: George Fitzgerald [George.Fitzgerald%x%accelrys.com] --_000_55AC410F3302E740AC9EC50011F73E8F041AB9299CEXCH1COLOacce_ Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: base64 SW50ZXJlc3RpbmcgdGhhdCB0aGlzIGxpbmsgaXMgbm8gbG9uZ2VyIGFjdGl2ZS4gSXQgcmVkaXJl Y3RzIHRvIGJvb2tzLmdvb2dsZS5jb20NCg0KDQoNCkZyb206IG93bmVyLWNoZW1pc3RyeStnZml0 emdlcmFsZD09YWNjZWxyeXMuY29tQGNjbC5uZXQgW21haWx0bzpvd25lci1jaGVtaXN0cnkrZ2Zp dHpnZXJhbGQ9PWFjY2VscnlzLmNvbUBjY2wubmV0XSBPbiBCZWhhbGYgT2YgUHJhc2hhbnQgU2lu Z2ggUmFuYSBwc3JhbmFbLV1nbWFpbC5jb20NClNlbnQ6IFN1bmRheSwgQXByaWwgMjIsIDIwMTIg MTA6NTEgQU0NClRvOiBHZW9yZ2UgRml0emdlcmFsZA0KU3ViamVjdDogQ0NMOiBHb29kIHNpdGUg Zm9yIGZpbmRpbmcgYm9va3MgKCBTZWFyY2ggYW5kIERvd25sb2FkIGRpcmVjdGx5KQ0KDQpHb29k IHNpdGUgZm9yIGZpbmRpbmcgYm9va3MgKCBTZWFyY2ggYW5kIERvd25sb2FkIGRpcmVjdGx5KQ0K DQpodHRwOi8vZnJlZS1ib29rcy51cy50by8NCg0KDQotLQ0KVGhhbmtzICYgUmVnYXJkcw0KDQpQ cmFzaGFudCBTaW5naCBSYW5hDQpQaEQgUmVzZWFyY2ggU2Nob2xhcg0KRGVwYXJ0bWVudCBvZiBJ bmZvcm1hdGlvbiAmIENvbW11bmljYXRpb24gVGVjaG5vbG9neQ0KQUJWLUluZGlhbiBJbnN0aXR1 dGUgb2YgSW5mb3JtYXRpb24gVGVjaG5vbG9neSAmIE1hbmFnZW1lbnQgKElJSVRNKSwgR3dhbGlv ciwgTVAsIEluZGlhLg0KDQpDb250YWN0OiAgKzkxLTkwOTgyMzY5OTcNCiAgICAgICAgICAgICAg ICs5MS05MzEzODg5OTMyDQpFbWFpbCAgIDogICBwc3JhbmF8LHxpaWl0bS5hYy5pbjxtYWlsdG86 cHNyYW5hfCx8aWlpdG0uYWMuaW4+DQogICAgICAgICAgICAgICAgcHNyYW5hfCx8Z21haWwuY29t PG1haWx0bzpwc3JhbmF8LHxnbWFpbC5jb20+DQoNCiJUcnkgdG8gRmFpbCwgQlVUIERvbid0IEZh aWwgdG8gVHJ5Ig0K --_000_55AC410F3302E740AC9EC50011F73E8F041AB9299CEXCH1COLOacce_ Content-Type: text/html; charset="utf-8" Content-Transfer-Encoding: base64 PGh0bWwgeG1sbnM6dj0idXJuOnNjaGVtYXMtbWljcm9zb2Z0LWNvbTp2bWwiIHhtbG5zOm89InVy bjpzY2hlbWFzLW1pY3Jvc29mdC1jb206b2ZmaWNlOm9mZmljZSIgeG1sbnM6dz0idXJuOnNjaGVt YXMtbWljcm9zb2Z0LWNvbTpvZmZpY2U6d29yZCIgeG1sbnM6bT0iaHR0cDovL3NjaGVtYXMubWlj cm9zb2Z0LmNvbS9vZmZpY2UvMjAwNC8xMi9vbW1sIiB4bWxucz0iaHR0cDovL3d3dy53My5vcmcv VFIvUkVDLWh0bWw0MCI+PGhlYWQ+PG1ldGEgaHR0cC1lcXVpdj1Db250ZW50LVR5cGUgY29udGVu dD0idGV4dC9odG1sOyBjaGFyc2V0PXV0Zi04Ij48bWV0YSBuYW1lPUdlbmVyYXRvciBjb250ZW50 PSJNaWNyb3NvZnQgV29yZCAxNCAoZmlsdGVyZWQgbWVkaXVtKSI+PHN0eWxlPjwhLS0NCi8qIEZv bnQgRGVmaW5pdGlvbnMgKi8NCkBmb250LWZhY2UNCgl7Zm9udC1mYW1pbHk6Q2FsaWJyaTsNCglw YW5vc2UtMToyIDE1IDUgMiAyIDIgNCAzIDIgNDt9DQpAZm9udC1mYWNlDQoJe2ZvbnQtZmFtaWx5 OlRhaG9tYTsNCglwYW5vc2UtMToyIDExIDYgNCAzIDUgNCA0IDIgNDt9DQovKiBTdHlsZSBEZWZp bml0aW9ucyAqLw0KcC5Nc29Ob3JtYWwsIGxpLk1zb05vcm1hbCwgZGl2Lk1zb05vcm1hbA0KCXtt YXJnaW46MGluOw0KCW1hcmdpbi1ib3R0b206LjAwMDFwdDsNCglmb250LXNpemU6MTIuMHB0Ow0K CWZvbnQtZmFtaWx5OiJUaW1lcyBOZXcgUm9tYW4iLCJzZXJpZiI7fQ0KYTpsaW5rLCBzcGFuLk1z b0h5cGVybGluaw0KCXttc28tc3R5bGUtcHJpb3JpdHk6OTk7DQoJY29sb3I6Ymx1ZTsNCgl0ZXh0 LWRlY29yYXRpb246dW5kZXJsaW5lO30NCmE6dmlzaXRlZCwgc3Bhbi5Nc29IeXBlcmxpbmtGb2xs b3dlZA0KCXttc28tc3R5bGUtcHJpb3JpdHk6OTk7DQoJY29sb3I6cHVycGxlOw0KCXRleHQtZGVj b3JhdGlvbjp1bmRlcmxpbmU7fQ0Kc3Bhbi5FbWFpbFN0eWxlMTcNCgl7bXNvLXN0eWxlLXR5cGU6 cGVyc29uYWwtcmVwbHk7DQoJZm9udC1mYW1pbHk6IkNhbGlicmkiLCJzYW5zLXNlcmlmIjsNCglj b2xvcjojMUY0OTdEO30NCi5Nc29DaHBEZWZhdWx0DQoJe21zby1zdHlsZS10eXBlOmV4cG9ydC1v bmx5Ow0KCWZvbnQtZmFtaWx5OiJDYWxpYnJpIiwic2Fucy1zZXJpZiI7fQ0KQHBhZ2UgV29yZFNl Y3Rpb24xDQoJe3NpemU6OC41aW4gMTEuMGluOw0KCW1hcmdpbjoxLjBpbiAxLjBpbiAxLjBpbiAx LjBpbjt9DQpkaXYuV29yZFNlY3Rpb24xDQoJe3BhZ2U6V29yZFNlY3Rpb24xO30NCi0tPjwvc3R5 bGU+PCEtLVtpZiBndGUgbXNvIDldPjx4bWw+DQo8bzpzaGFwZWRlZmF1bHRzIHY6ZXh0PSJlZGl0 IiBzcGlkbWF4PSIxMDI2IiAvPg0KPC94bWw+PCFbZW5kaWZdLS0+PCEtLVtpZiBndGUgbXNvIDld Pjx4bWw+DQo8bzpzaGFwZWxheW91dCB2OmV4dD0iZWRpdCI+DQo8bzppZG1hcCB2OmV4dD0iZWRp dCIgZGF0YT0iMSIgLz4NCjwvbzpzaGFwZWxheW91dD48L3htbD48IVtlbmRpZl0tLT48L2hlYWQ+ PGJvZHkgbGFuZz1FTi1VUyBsaW5rPWJsdWUgdmxpbms9cHVycGxlPjxkaXYgY2xhc3M9V29yZFNl Y3Rpb24xPjxwIGNsYXNzPU1zb05vcm1hbD48c3BhbiBzdHlsZT0nZm9udC1zaXplOjExLjBwdDtm b250LWZhbWlseToiQ2FsaWJyaSIsInNhbnMtc2VyaWYiO2NvbG9yOiMxRjQ5N0QnPkludGVyZXN0 aW5nIHRoYXQgdGhpcyBsaW5rIGlzIG5vIGxvbmdlciBhY3RpdmUuIEl0IHJlZGlyZWN0cyB0byBi b29rcy5nb29nbGUuY29tPG86cD48L286cD48L3NwYW4+PC9wPjxwIGNsYXNzPU1zb05vcm1hbD48 c3BhbiBzdHlsZT0nZm9udC1zaXplOjExLjBwdDtmb250LWZhbWlseToiQ2FsaWJyaSIsInNhbnMt c2VyaWYiO2NvbG9yOiMxRjQ5N0QnPjxvOnA+Jm5ic3A7PC9vOnA+PC9zcGFuPjwvcD48cCBjbGFz cz1Nc29Ob3JtYWw+PHNwYW4gc3R5bGU9J2ZvbnQtc2l6ZToxMS4wcHQ7Zm9udC1mYW1pbHk6IkNh bGlicmkiLCJzYW5zLXNlcmlmIjtjb2xvcjojMUY0OTdEJz48bzpwPiZuYnNwOzwvbzpwPjwvc3Bh bj48L3A+PHAgY2xhc3M9TXNvTm9ybWFsPjxzcGFuIHN0eWxlPSdmb250LXNpemU6MTEuMHB0O2Zv bnQtZmFtaWx5OiJDYWxpYnJpIiwic2Fucy1zZXJpZiI7Y29sb3I6IzFGNDk3RCc+PG86cD4mbmJz cDs8L286cD48L3NwYW4+PC9wPjxwIGNsYXNzPU1zb05vcm1hbD48Yj48c3BhbiBzdHlsZT0nZm9u dC1zaXplOjEwLjBwdDtmb250LWZhbWlseToiVGFob21hIiwic2Fucy1zZXJpZiInPkZyb206PC9z cGFuPjwvYj48c3BhbiBzdHlsZT0nZm9udC1zaXplOjEwLjBwdDtmb250LWZhbWlseToiVGFob21h Iiwic2Fucy1zZXJpZiInPiBvd25lci1jaGVtaXN0cnkrZ2ZpdHpnZXJhbGQ9PWFjY2VscnlzLmNv bUBjY2wubmV0IFttYWlsdG86b3duZXItY2hlbWlzdHJ5K2dmaXR6Z2VyYWxkPT1hY2NlbHJ5cy5j b21AY2NsLm5ldF0gPGI+T24gQmVoYWxmIE9mIDwvYj5QcmFzaGFudCBTaW5naCBSYW5hIHBzcmFu YVstXWdtYWlsLmNvbTxicj48Yj5TZW50OjwvYj4gU3VuZGF5LCBBcHJpbCAyMiwgMjAxMiAxMDo1 MSBBTTxicj48Yj5Ubzo8L2I+IEdlb3JnZSBGaXR6Z2VyYWxkPGJyPjxiPlN1YmplY3Q6PC9iPiBD Q0w6IEdvb2Qgc2l0ZSBmb3IgZmluZGluZyBib29rcyAoIFNlYXJjaCBhbmQgRG93bmxvYWQgZGly ZWN0bHkpPG86cD48L286cD48L3NwYW4+PC9wPjxwIGNsYXNzPU1zb05vcm1hbD48bzpwPiZuYnNw OzwvbzpwPjwvcD48cCBjbGFzcz1Nc29Ob3JtYWw+R29vZCBzaXRlIGZvciBmaW5kaW5nIGJvb2tz ICggU2VhcmNoIGFuZCBEb3dubG9hZCBkaXJlY3RseSk8YnI+PGJyPjxhIGhyZWY9Imh0dHA6Ly9m cmVlLWJvb2tzLnVzLnRvLyI+aHR0cDovL2ZyZWUtYm9va3MudXMudG8vPC9hPjxicj48YnIgY2xl YXI9YWxsPjxicj4tLSA8YnI+VGhhbmtzICZhbXA7IFJlZ2FyZHM8YnI+PGJyPlByYXNoYW50IFNp bmdoIFJhbmE8YnI+UGhEIFJlc2VhcmNoIFNjaG9sYXI8YnI+RGVwYXJ0bWVudCBvZiBJbmZvcm1h dGlvbiAmYW1wOyBDb21tdW5pY2F0aW9uIFRlY2hub2xvZ3k8YnI+QUJWLUluZGlhbiBJbnN0aXR1 dGUgb2YgSW5mb3JtYXRpb24gVGVjaG5vbG9neSAmYW1wOyBNYW5hZ2VtZW50IChJSUlUTSksIEd3 YWxpb3IsIE1QLCBJbmRpYS48YnI+PGJyPkNvbnRhY3Q6Jm5ic3A7ICs5MS05MDk4MjM2OTk3PGJy PiZuYnNwOyAmbmJzcDsgJm5ic3A7ICZuYnNwOyAmbmJzcDsgJm5ic3A7ICZuYnNwOyZuYnNwOyAr OTEtOTMxMzg4OTkzMjxicj5FbWFpbCZuYnNwOyZuYnNwOyA6Jm5ic3A7Jm5ic3A7IDxhIGhyZWY9 Im1haWx0bzpwc3JhbmF8LHxpaWl0bS5hYy5pbiIgdGFyZ2V0PSJfYmxhbmsiPnBzcmFuYXwsfGlp aXRtLmFjLmluPC9hPjxicj4mbmJzcDsgJm5ic3A7ICZuYnNwOyAmbmJzcDsgJm5ic3A7ICZuYnNw OyAmbmJzcDsgJm5ic3A7IDxhIGhyZWY9Im1haWx0bzpwc3JhbmF8LHxnbWFpbC5jb20iIHRhcmdl dD0iX2JsYW5rIj5wc3JhbmF8LHxnbWFpbC5jb208L2E+PGJyPjxicj4mcXVvdDtUcnkgdG8gRmFp bCwgQlVUIERvbid0IEZhaWwgdG8gVHJ5JnF1b3Q7PG86cD48L286cD48L3A+PC9kaXY+PC9ib2R5 PjwvaHRtbD4= --_000_55AC410F3302E740AC9EC50011F73E8F041AB9299CEXCH1COLOacce_-- From owner-chemistry@ccl.net Mon Apr 23 14:19:00 2012 From: "Daniele Dondi kaliumster()gmail.com" To: CCL Subject: CCL: Gaussview dipole moments Message-Id: <-46768-120423140320-20815-OjX3q0MdmCA5hyvQBk7nPw]*[server.ccl.net> X-Original-From: Daniele Dondi Content-Type: multipart/alternative; boundary=f46d04463182b555c604be5c73f7 Date: Mon, 23 Apr 2012 20:03:14 +0200 MIME-Version: 1.0 Sent to CCL by: Daniele Dondi [kaliumster^^^gmail.com] --f46d04463182b555c604be5c73f7 Content-Type: text/plain; charset=ISO-8859-1 Click on view file (or open the output file with a text editor) and search the string "Dipole moment (field-independent basis, Debye" DD 2012/4/23 Robert A Lewis R.A.Lewis###hull.ac.uk > I am running Gaussview 5.0 with Guassian 09W. The output from charge > calculations gives the net dipole moment and a graphical output but not the > x,y, and z components. How can this information be obtained?**** > > ** ** > > Regards**** > > ** ** > > ** ** > > Rob Lewis**** > > ** ** > > ** ** > > ** ** > > Dr Robert A. Lewis**** > > Department of Chemistry**** > > University of Hull**** > > Cottingham Road**** > > Hull HU6 7RX**** > > T +44 (0)1482 466649**** > > F +44(0)1482 466410**** > > email: R.A.Lewis__hull.ac.uk**** > > ** ** > > ************************************************** > To view the terms under which this email is > distributed, please go to > http://www2.hull.ac.uk/legal/disclaimer.aspx > ************************************************** > --f46d04463182b555c604be5c73f7 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Click on view file (or open the output file with= a text editor) and search the string "Dipole moment (field-independen= t basis, Debye"

DD

2012/4/23 = Robert A Lewis R.A.Lewis###hull.ac.uk <owner-chemistry__ccl.net>

I am running Gaussview 5.0 with Guassian= 09W. The output from charge calculations gives the net dipole moment and a= graphical output but not the x,y, and z components. How can this informati= on be obtained?

=A0

Regards<= u>

=A0

=A0

Rob Lewis

=A0

=A0

=A0

Dr Robert A. Lew= is

Department of Chemistry

University of Hull

Cottingham Road<= u>

Hull=A0 HU6 7RX

T +44 (0)1482 466649

F +44(0)1482 466410

email: R.A.Lewis__hull.ac.uk

=A0


***************= ***********************************
To view the terms under which this email is
distributed, please go to
= http://www2.hull.ac.uk/legal/disclaimer.aspx
**************************************************
--f46d04463182b555c604be5c73f7-- From owner-chemistry@ccl.net Mon Apr 23 14:55:00 2012 From: "Wolf Ihlenfeldt wdi .. xemistry.com" To: CCL Subject: CCL: free software for calculation of TPSA or PSA for ligands databases Message-Id: <-46769-120423135617-13901-fsHEPFm9WwaJ/i0gKnUGVw_._server.ccl.net> X-Original-From: Wolf Ihlenfeldt Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Mon, 23 Apr 2012 19:56:10 +0200 MIME-Version: 1.0 Sent to CCL by: Wolf Ihlenfeldt [wdi!A!xemistry.com] Easily done with a tiny Cactvs script (www.xemistry.com/academic for free academic downloads) ---snip-- set th [table create] table addcol $th E_SMILES table addcol $th E_TPSA molfile hloop [lindex $argv 0] eh { table addens $th $eh } table sort $th {E_TPSA ascending} table write $th tpsa.tsv --snip-- Run as 'csts -f script.tcl structurefile'. Of course the table output format, additional columns, etc. can be further customized. The script automatically detects the input format, so you can process SMILES, SDF, SLN, Mol2, or any other multi-record format without change. On Mon, Apr 23, 2012 at 2:01 PM, Andrew Voronkov drugdesign++yandex.ru wrote: > > Sent to CCL by: Andrew Voronkov [drugdesign[-]yandex.ru] > Dear CCL users, can anyone recommend free software for TPSA calculation where I can load database of ligands, for example several hundreds and ideally get the ranked according PSA. I am using now free Molinspiration server, but there is no file upload option, onl one by one option. Best regards, Andrew>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > -- Wolf-D. Ihlenfeldt -  Xemistry GmbH - wdi**xemistry.com Phone: +49 6174 201455 - Fax +49 6174 209665 --- xemistry gmbh – Geschäftsführer/Managing Director: Dr. W. D. Ihlenfeldt Address: Hainholzweg 11, D-61462 Königstein, Germany HR Königstein B7522 : Ust/VAT ID DE215316329 : DUNS 34-400-1719 From owner-chemistry@ccl.net Mon Apr 23 15:30:00 2012 From: "David A Mannock dmannock],[ualberta.ca" To: CCL Subject: CCL:G: creating a formatted .fchk file in gaussian Message-Id: <-46770-120423142441-20892-43h8eXmuNQNdqi/yCtRj2g.@.server.ccl.net> X-Original-From: David A Mannock Content-Type: multipart/alternative; boundary=f46d043d6567df789504be5cbf75 Date: Mon, 23 Apr 2012 12:24:32 -0600 MIME-Version: 1.0 Sent to CCL by: David A Mannock [dmannock[#]ualberta.ca] --f46d043d6567df789504be5cbf75 Content-Type: text/plain; charset=ISO-8859-1 If memory serves, you have to do this change in format on the same computer on which the calculation was performed, then download the files to your workstation. Dave On Sun, Apr 22, 2012 at 1:44 AM, Haya Kornweitz hayak]|[ariel.ac.il < owner-chemistry^^ccl.net> wrote: > > Sent to CCL by: "Haya Kornweitz" [hayak _ ariel.ac.il] > Dear CCls can you help me please? > I try to create Formatted Checkpoint Files using g03 or g09 using the > command: > formchk filel.chk filel.fchk as recommended in gaussian's manual, > but after about 50 lines I get an announcement: > Segmentation fault > Error termination in NtrErr: > ntran open failure returned to fopen. > > I get the same announcement for several chk file, all correct chk files I > can use them to begin a new calculation correctly. > > Gratefully > Haya> > > --f46d043d6567df789504be5cbf75 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
If memory serves, you have to do this change in = format on the same computer on which the calculation was performed, then do= wnload the files to your workstation. Dave

On Sun, Apr 22, 2012 at 1:44 AM, Haya Kornweitz hayak]|[ariel.ac.il <owner-chemistry^^ccl.net> = wrote:

Sent to CCL by: "Haya =A0Kornweitz" [hayak _ ariel.ac.il]
Dear CCls can you help me please?
I try to create Formatted Checkpoint Files using g03 or g09 using the comma= nd:
formchk filel.chk filel.fchk as recommended in gaussian's manual,
but after about 50 lines I get an announcement:
=A0Segmentation fault
Error termination in NtrErr:
=A0ntran open failure returned to fopen.

I get the same announcement for several chk file, all correct chk files =A0= I can use them to begin a new calculation correctly.

Gratefully
Haya



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY^^ccl.n= et or use:
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEM= ISTRY-REQUEST^^ccl.net or use
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

Subscribe/Unsubscribe:
=A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.n= et/jobs
Conferences: http://server.ccl.net/chemistry/announcements/co= nferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
=A0 =A0 =A0h= ttp://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/



--f46d043d6567df789504be5cbf75-- From owner-chemistry@ccl.net Mon Apr 23 18:18:00 2012 From: "sumit sumitkrmgr#gmail.com" To: CCL Subject: CCL:G: problwm in saving image in gaussview 4.1(visualization software for gaussian G03) Message-Id: <-46771-120423072710-1232-iuhTQn2FpfQCL0g+OMqxjw%a%server.ccl.net> X-Original-From: sumit Content-Type: multipart/alternative; boundary=001636c928c0ee9d8f04be56eac6 Date: Mon, 23 Apr 2012 16:57:04 +0530 MIME-Version: 1.0 Sent to CCL by: sumit [sumitkrmgr]_[gmail.com] --001636c928c0ee9d8f04be56eac6 Content-Type: text/plain; charset=UTF-8 Hi, I am sumit from IISER Pune. I am facing problem in saving image in Gauss View 4.1.0 (visualization software for gaussian G03). when I am saving image in any format (tiff, jpg, bmp, etc..), computer restarts its own. I am not understanding the fault. Please help me in solving this problem. thank You, Sumit *----------------------------------------------------------------* *Sumit Kumar Research Scholar IISER PUNE* *----------------------------------------------------------------* --001636c928c0ee9d8f04be56eac6 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hi,
I am sumit from IISER Pune.
I am facing problem in saving image i= n Gauss View 4.1.0 (visualization software for gaussian G03).
when I am= saving image in any format (tiff, jpg, bmp, etc..), computer restarts its = own.
I am not understanding the fault.
Please help me in solving this problem= .


thank You,
Sumit
-------------------------------------= ---------------------------
Sumit Kumar
Resea= rch Scholar
IISER PUNE
-------------------------------= ---------------------------------

--001636c928c0ee9d8f04be56eac6-- From owner-chemistry@ccl.net Mon Apr 23 18:53:00 2012 From: "David LAGORCE david.lagorce ~ inserm.fr" To: CCL Subject: CCL: free software for calculation of TPSA or PSA for ligands databases Message-Id: <-46772-120423134023-21830-VCjg7WvqRuSdtEA8cdS1Bw{=}server.ccl.net> X-Original-From: David LAGORCE Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8 Date: Mon, 23 Apr 2012 19:40:11 +0200 Mime-Version: 1.0 (1.0) Sent to CCL by: David LAGORCE [david.lagorce a inserm.fr] dear colleagues, you can use the FAF-Drugs2 web server which can compute (among others) tPSA (ertl et al) on 50000 molecules maximum. That web-server (embedding OpenBabel libraries) is available at http://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py?form=FAF-Drugs2 David LAGORCE Le 23 avr. 2012 à 17:32, "Geoffrey Hutchison geoffh*pitt.edu" a écrit : > > Sent to CCL by: Geoffrey Hutchison [geoffh a pitt.edu] >> Dear CCL users, can anyone recommend free software for TPSA calculation where I can load database of ligands, for example several hundreds and ideally get the ranked according PSA. I am using now free Molinspiration server, but there is no file upload option, onl one by one option. Best regards, Andrew > > There are undoubtedly multiple programs can do this, but this can be done simply with Open Babel: > > % Output as SMILES, sorted by TPSA and append the TPSA value to the title > obabel ~/data/drugbank-ca.sdf --append TPSA --sort TPSA -O ~/data/db-sorted.smi > > % Or sort by TPSA, but add a SDF property field with the TPSA value > obabel ~/data/drugbank-ca.sdf --sort TPSA --add TPSA -O ~/data/db-sorted.sdf > > Of course you can get it at http://openbabel.org/ > > Hope that helps, > -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 Apr 23 19:28:00 2012 From: "Rajarshi Guha rajarshi.guha|-|gmail.com" To: CCL Subject: CCL: free software for calculation of TPSA or PSA for ligands databases Message-Id: <-46773-120423153308-6707-FgpsrE6QyLVUcmKZmnBtAA^^server.ccl.net> X-Original-From: Rajarshi Guha Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 23 Apr 2012 15:33:01 -0400 MIME-Version: 1.0 Sent to CCL by: Rajarshi Guha [rajarshi.guha++gmail.com] The CDKDescUI will do this (it also has a command line mode that can be used in a server environment) http://rguha.net/code/java/cdkdesc.html On Mon, Apr 23, 2012 at 8:01 AM, Andrew Voronkov drugdesign++yandex.ru wrote: > > Sent to CCL by: Andrew Voronkov [drugdesign[-]yandex.ru] > Dear CCL users, can anyone recommend free software for TPSA calculation where I can load database of ligands, for example several hundreds and ideally get the ranked according PSA. I am using now free Molinspiration server, but there is no file upload option, onl one by one option. Best regards, Andrew>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > -- Rajarshi Guha | http://blog.rguha.net NIH Center for Advancing Translational Science From owner-chemistry@ccl.net Mon Apr 23 20:03:00 2012 From: "Sumit kumar sumitkrmgr-*-gmail.com" To: CCL Subject: CCL:G: problem in saving image in gaussview 4.1 Message-Id: <-46774-120423154437-4605-23DHtfsdS4rk8aDhoEzzpg%x%server.ccl.net> X-Original-From: "Sumit kumar" Date: Mon, 23 Apr 2012 15:44:35 -0400 Sent to CCL by: "Sumit kumar" [sumitkrmgr__gmail.com] Hi, I am sumit from IISER Pune. I am facing problem in saving image in Gauss View 4.1.0 (visualization software for gaussian G03). when I am saving image in any format (tiff, jpg, bmp, etc..), computer restarts its own. I am not understanding the fault. Please help me in solving this problem. thank You, Sumit ---------------------------------------------------------------- Sumit Kumar Research Scholar IISER PUNE ---------------------------------------------------------------- From owner-chemistry@ccl.net Mon Apr 23 20:38:00 2012 From: "Kyle Lutz kyle.r.lutz,,gmail.com" To: CCL Subject: CCL: free software for calculation of TPSA or PSA for ligands databases Message-Id: <-46775-120423202139-3303-I0wan5JuQk9EydnR84yNPA**server.ccl.net> X-Original-From: Kyle Lutz Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252 Date: Mon, 23 Apr 2012 20:21:29 -0400 MIME-Version: 1.0 Sent to CCL by: Kyle Lutz [kyle.r.lutz^gmail.com] Hi Andrew, You can do this quite easily using chemkit's (http://www.chemkit.org) python API as follows: --- tpsa-sort.py ----------------------------------------------------------------------- import sys import chemkit # open and read file file = chemkit.MoleculeFile(sys.argv[1]) file.read() # calculate tpsa values values = [] for molecule in file.molecules(): values.append((molecule.descriptor("tpsa"), molecule)) # print sorted tpsa values and the names of the molecules for tpsa, molecule in sorted(values): print "%f, %s" % (tpsa, molecule.name()) --- end tpsa-sort.py ------------------------------------------------------------------ This can also be extended to sort by any of the other molecular descriptors that chemkit can calculate by changing the "tpsa" string to another descriptor name. See http://wiki.chemkit.org/Features#Molecular_Descriptors for a list of available descriptors. Cheers, Kyle On Mon, Apr 23, 2012 at 1:56 PM, Wolf Ihlenfeldt wdi .. xemistry.com wrote: > > Sent to CCL by: Wolf Ihlenfeldt [wdi!A!xemistry.com] > Easily done with a tiny Cactvs script (www.xemistry.com/academic for > free academic downloads) > > ---snip-- > set th [table create] > table addcol $th E_SMILES > table addcol $th E_TPSA > molfile hloop [lindex $argv 0] eh { >        table addens $th $eh > } > table sort $th {E_TPSA ascending} > table write $th tpsa.tsv > --snip-- > > Run as 'csts -f script.tcl structurefile'. > > Of course the table output format, additional columns, etc. can be > further customized. The script automatically detects the input format, > so you can process SMILES, SDF, SLN, Mol2, or any other multi-record > format without change. > > > > > > On Mon, Apr 23, 2012 at 2:01 PM, Andrew Voronkov drugdesign++yandex.ru > wrote: >> >> Sent to CCL by: Andrew Voronkov [drugdesign[-]yandex.ru] >> Dear CCL users, can anyone recommend free software for TPSA calculation where I can load database of ligands, for example several hundreds and ideally get the ranked according PSA. I am using now free Molinspiration server, but there is no file upload option, onl one by one option. Best regards, Andrew>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> >> > > > > -- > Wolf-D. Ihlenfeldt -  Xemistry GmbH - wdi-,-xemistry.com > Phone: +49 6174 201455 - Fax +49 6174 209665 > --- > xemistry gmbh – Geschäftsführer/Managing Director: Dr. W. D. Ihlenfeldt > Address: Hainholzweg 11, D-61462 Königstein, Germany > HR Königstein B7522 : Ust/VAT ID DE215316329 : DUNS 34-400-1719>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > From owner-chemistry@ccl.net Mon Apr 23 22:34:00 2012 From: "Hoa Thi My Pham hoahoa9h(!)gmail.com" To: CCL Subject: CCL:G: Find the TS of SN1 reaction Message-Id: <-46776-120423222226-6203-HPX2Rwt9q5nYQeRkWcA16Q##server.ccl.net> X-Original-From: "Hoa Thi My Pham" Date: Mon, 23 Apr 2012 22:22:24 -0400 Sent to CCL by: "Hoa Thi My Pham" [hoahoa9h(_)gmail.com] Dear sir, I'm Hoa Vietnam. I calculate the TS berny of the first step of SN1 reaction with the input file %chk=QST2.chk %mem=20MW %nproc=2 # opt=(calcfc,ts) b3lyp/3-21+g* scrf=(solvent=water) nosymm geom=connectivity scf=tight products 0 1 C C 1 B1 H 2 B2 1 A1 H 2 B3 1 A2 3 D1 H 2 B4 1 A3 3 D2 C 1 B5 2 A4 4 D3 H 6 B6 1 A5 2 D4 H 6 B7 1 A6 2 D5 H 6 B8 1 A7 2 D6 C 1 B9 2 A8 6 D7 H 10 B10 1 A9 2 D8 H 10 B11 1 A10 2 D9 H 10 B12 1 A11 2 D10 Cl 10 B13 1 A12 2 D11 B1 1.46623896 B2 1.10047117 B3 1.09146452 B4 1.11194865 B5 1.46653896 B6 1.11136264 B7 1.09065854 B8 1.10162669 B9 1.46556055 B10 1.11345303 B11 1.09192814 B12 1.09950011 B13 4.45070089 A1 111.01703990 A2 113.89401353 A3 106.44848477 A4 119.79618326 A5 106.70753530 A6 114.13497825 A7 110.76672326 A8 119.89172728 A9 106.91273529 A10 113.67602938 A11 110.99906560 A12 109.86927454 D1 127.57448951 D2 -112.84746242 D3 -11.23284242 D4 69.38542419 D5 -170.09739800 D6 -42.99559059 D7 178.66179578 D8 -107.85114836 D9 11.22182606 D10 138.52452321 D11 -87.32787440 1 2 1.0 6 1.0 10 1.0 2 3 1.0 4 1.0 5 1.0 3 4 5 6 7 1.0 8 1.0 9 1.0 7 8 9 10 11 1.0 12 1.0 13 1.0 11 12 13 14 And i have an error BRING ME INTO THE COMPANY OF THOSE WHO SEEK TRUTH, AND DELIVER ME FROM THOSE WHO HAVE FOUND IT. Error termination request processed by link 9999. Error termination via Lnk1e in C:\G03W\l9999.exe at Tue Apr 24 09:14:17 2012. Job cpu time: 0 days 0 hours 17 minutes 43.0 seconds. File lengths (MBytes): RWF= 88 Int= 0 D2E= 0 Chk= 17 Scr= 1 I don't know why. Please help me. Thanks so much