From owner-chemistry@ccl.net Fri Nov 9 02:47:00 2007 From: "Giulia Caron giulia.caron++unito.it" To: CCL Subject: CCL: CONVERTING CNT OR GRD CONTOUR MAPS IN FORMATS IMPORTABLE IN PYMOL Message-Id: <-35570-071108113311-28552-d3jRwebDKMPwr3DYJMgDWQ-x-server.ccl.net> X-Original-From: "Giulia Caron" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Thu, 8 Nov 2007 16:59:14 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: "Giulia Caron" [giulia.caron!A!unito.it] Hello, try with BIOCUBE (www.casmedchem.unito.it) which is free for academic institutions Giulia Caron -- Giulia Caron PhD Dipartimento di Scienza e Tecnologia del Farmaco via Giuria 9 10125 Torino (Italy) www.casmedchem.unito.it www.personalweb.unito.it/giulia.caron > > > -------------------------- Messaggio originale --------------------------- > Oggetto: CCL: CONVERTING CNT OR GRD CONTOUR MAPS IN FORMATS IMPORTABLE IN > PYMOL > Da: "Paola Tedeschi tedeschipaola _ libero.it" > > Data: Gio, 8 Novembre 2007, 10:06 am > A: "Caron, Giulia " > -------------------------------------------------------------------------- > > > Sent to CCL by: "Paola Tedeschi" [tedeschipaola\a/libero.it] > Dear CCL, > I am interested in converting cnt or grd contour maps generated with > GRID-GOLPE in a format properly importable in pymol for a better > rendering. > I noticed that pymol was able to read grd files coming from GRID-GOLPE but > however the maps seems to be flatten and their appearance is rather > diverse from what I see in Sybyl. > The problem could be that GRID-GOLPE grd could be of molcad format while > pymol seems to prefer the insight format. > Does anybody know if some free tool exist to convert this format in one > properly readable by pymol? > > Thanks in advance > Paola> > > > From owner-chemistry@ccl.net Fri Nov 9 10:53:01 2007 From: "Alex Allardyce aa|-|chemaxon.com" To: CCL Subject: CCL: Requesting software Message-Id: <-35571-071109104517-10146-7dTr0ypoI29Ksm/XxS3uXg(a)server.ccl.net> X-Original-From: Alex Allardyce Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 09 Nov 2007 09:54:15 -0500 MIME-Version: 1.0 Sent to CCL by: Alex Allardyce [aa[A]chemaxon.com] HI Mohan, Instant JChem will do all this, infact you can have each parameter separately and another field which combines the parameters to give a simple yes/no indication of 'likeness'. The application will run on all major operating systems and comes with it's own database engine - so you can search/manage and merge additional data or add new data rows (which will cause structure based prediction columns to be auto populated). For more information and download see: http://www.chemaxon.com/product/ijc.html Instant JChem Personal is free but does not include the licenses to enable structure based prediction. For academic users you can obtain all the keys to enable this (and all of our software) for free, see this link for more information and signup: http://www.chemaxon.com/acpack_conditions.html Cheers Alex Mohana Sundharam Velayutham mohanrocksu*|*gmail.com wrote: > Sent to CCL by: "Mohana Sundharam Velayutham" [mohanrocksu,,gmail.com] > Dear Concerned, > > My name is Mohan. I'm novice in this field and i've list of chemicals in a SDF file. I want freeware application which could calculate the Lipinski Parameters for the chemicals in the SDF file. Please guide me where i can find it. Thanks in advance. My mail ID is info.:.pharmolae.com > > Regards, > Mohan> > > > -- Alex Allardyce Dir. Marketing, ChemAxon Cell-US: 1-857-544-0541 skype: alex_allardyce From owner-chemistry@ccl.net Fri Nov 9 11:36:00 2007 From: "Rob Noble-Eddy r.noble-eddy**ed.ac.uk" To: CCL Subject: CCL:G: Guassian - Hindered rotor frequency option Message-Id: <-35572-071109093408-23553-iekOJY43JXBWhoLZsgeQCw_+_server.ccl.net> X-Original-From: "Rob Noble-Eddy" Date: Fri, 9 Nov 2007 09:34:04 -0500 Sent to CCL by: "Rob Noble-Eddy" [r.noble-eddy^-^ed.ac.uk] Hi, I have a molecule which contains a phenyl group, and want to calculate the free energies of its two conformers. The barrier to rotation of the phenyl group is around kT and so I believe any estimation of the free energy should include this rotation, rather than simply using a standard frequency calculation on the equilibrium position. I tried to use the freq=hinderedrotor option in gaussian '03 to achieve this, but after successfully completing a geometry optimisation it starts to do the frequency calculation, but stops with an error when it tries to determine if there are any hindered rotors in the molecule. I've included the output below, if anyone has any ideas, or has used this feature before please get in touch. Thanks, Rob ============================================ Internal coordinate list checked Check for planar centers 1 2 3 7 359.997 2 1 4 9 360.000 3 1 5 10 360.000 4 2 6 11 360.000 5 3 6 12 360.000 6 4 5 13 360.000 Check reduced barrier height. Cut-off : V/RT = 33.7561 Check for ring deformation Number of internal rotation degrees of freedom = 2 NNew= 36 NTest= 2 NB= 8 IFrz= 0 IBar= 0 ICyc= 0 Problem with the number of degrees of freedom Error termination via Lnk1e in /usr/local/Chem-Apps/g03_d01/g03/l716.exe at Fri Nov 9 11:29:03 2007. From owner-chemistry@ccl.net Fri Nov 9 12:11:00 2007 From: "Cong Wang wc0546[a]gmail.com" To: CCL Subject: CCL: Looking for Casimir-Polder type calculation program package Message-Id: <-35573-071109101858-7529-8p3/62L4ZFLtKBdTWfs0pA_+_server.ccl.net> X-Original-From: "Cong Wang" Date: Fri, 9 Nov 2007 10:18:55 -0500 Sent to CCL by: "Cong Wang" [wc0546^_^gmail.com] Hello everyone, I am looking for some program package can perform Casimir-Polder type calculation for dispersion interaction. It is better to have some flexibility that is possible to modify the formula of polarizability. I am grateful for any suggestions, thank you very much Best regards Cong Wang From owner-chemistry@ccl.net Fri Nov 9 12:45:01 2007 From: "Joe Kwiatkowski jk905{}imperial.ac.uk" To: CCL Subject: CCL:G: Gaussian - orthogonalising wavefunctions Message-Id: <-35574-071109123355-9640-suYs0sCwVKPnaZmanvpq3w-.-server.ccl.net> X-Original-From: Joe Kwiatkowski Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 09 Nov 2007 17:32:54 +0000 MIME-Version: 1.0 Sent to CCL by: Joe Kwiatkowski [jk905]-[imperial.ac.uk] Dear CCl'ers I am calculating the transfer integrals between molecules by projecting the orbitals of each isolated molecule onto the orbitals of the pair. To do this I need orthogonal orbitals. At the moment I am orthogonalising the orbitals myself with Lowdin's symmetric transformation. Is there anyway to convince Gaussian to do this for me? Thank you in advance, Joe -- Joe Kwiatkowski EXSS, Physics Imperial College London Prince Consort Road SW7 2BW Tel: 0207 594 6682 From owner-chemistry@ccl.net Fri Nov 9 16:15:00 2007 From: "Wang xie.wang .. gmail.com" To: CCL Subject: CCL:G: question about freezing coordinates in Gaussian Message-Id: <-35575-071109160834-10673-+2qddkiM/kaSHNq/67bhLQ ~~ server.ccl.net> X-Original-From: Wang Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 9 Nov 2007 15:08:32 -0500 MIME-Version: 1.0 Sent to CCL by: Wang [xie.wang]=[gmail.com] Dear all, Is there a way in gaussian to fix atomic x,y coordinates but allow z coordinate to relax in geometry optimization? Thanks a lot in advance! Wang From owner-chemistry@ccl.net Fri Nov 9 18:39:01 2007 From: "Naser Eltaher Eltayeb nasertaha90 . yahoo.co.uk" To: CCL Subject: CCL: Looking for program similar to AOMIX Message-Id: <-35576-071109183415-16196-MEAxJg+sxvq2MVgktdvekA|-|server.ccl.net> X-Original-From: "Naser Eltaher Eltayeb" Date: Fri, 9 Nov 2007 18:34:11 -0500 Sent to CCL by: "Naser Eltaher Eltayeb" [nasertaha90-#-yahoo.co.uk] Dear All I am looking for software can do the functions of AOMIX, any help welcome. AOMIX site www.sg-chem.net. thank you Naser Eltaher eltayeb Universiti Sains Malaysia From owner-chemistry@ccl.net Fri Nov 9 20:30:00 2007 From: "Chunsen Li chunsen_li:-:yahoo.com.cn" To: CCL Subject: CCL: =?gb2312?q?=BB=D8=B8=B4=A3=BA=20CCL:=20looking=20for=20a=20software=20for?= =?gb2312?q?=20displaying=20the=20molecular=20structures?= Message-Id: <-35577-071109162102-13629-23DHtfsdS4rk8aDhoEzzpg[a]server.ccl.net> X-Original-From: Chunsen Li Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-891977616-1194639644=:37343" Date: Sat, 10 Nov 2007 04:20:44 +0800 (CST) MIME-Version: 1.0 Sent to CCL by: Chunsen Li [chunsen_li**yahoo.com.cn] --0-891977616-1194639644=:37343 Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 8bit Hi Warren, Thanks. But I can't download this software since the download web can't not be opened. Can you show me anther web address of PyMOL? Regards, Chunsen "Warren DeLano warren:_:delsci.com" дµÀ£º Sent to CCL by: "Warren DeLano" [warren|,|delsci.com] Not sure, but PyMOL can get close: http://pymol.sf.net/pmimag/atomic.png However, it does take a bit of tweaking: set_color nitrogen, [0.6, 0.7, 1.0] fragment arg as spheres bg white show sticks set sphere_scale, 0.2 set stick_radius, 0.08 set stick_color, grey30 label not hydro, elem color grey90, elem c set label_color, black set antialias,3 set ray_trace_mode,1 viewport 400 zoom complete=1 ray http://pymol.sf.net open source code some builds are free > -----Original Message----- > From: owner-chemistry-*-ccl.net [mailto:owner-chemistry-*-ccl.net] > Sent: Tuesday, November 06, 2007 6:58 AM > To: Warren DeLano > Subject: CCL: looking for a software for displaying the > molecular structures > > > Sent to CCL by: "Chunsen Li" [chunsen_li!A!yahoo.com.cn] > Hi , > > I want know which software can display the molecular > structures as shown in Figure 1 of Angew. Chem. Int. Ed. > 2005, 44, 2939. > The bond in the structure is shown as single line and the > labels can be add in the center of the atoms freely. In > addition, the atoms can be in different patterns and colors. > The similar picture and be found from http://qc.physto.se/home.htm. > > Which software can do this? Is it free of charge? > > Thank you. > > > Chunsen Li > Center for Theoretical Chemistry, Department of Chemistry, > Xiamen University, Xiamen, 361005, China. > Tel.: 86-592-2180418 Fax: 86-592-2184708 > email: lics01]-[xmu.edu.cn chunsen_li]-[yahoo.com.cn 2007-10-30 > > > > -= 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 look up the X-Original-From: line > in the mail header.> > > Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, > Password: search) > > > > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt---------------------------------------- Chunsen Li Center for Theoretical Chemistry, Department of Chemistry, Xiamen University, Xiamen, 361005, China. Tel.: 86-592-2180418 Fax: 86-592-2184708 email: lics01 .. xmu.edu.cn chunsen_li .. yahoo.com.cn --------------------------------- ÑÅ»¢ÓÊÏ䣬ÖÕÉú»ï°é£¡ --0-891977616-1194639644=:37343 Content-Type: text/html; charset=gb2312 Content-Transfer-Encoding: 8bit
Hi Warren,
Thanks. But I can't download this software since the download web can't not be opened. Can you show me anther web address of PyMOL?
 
 
Regards,
 
 
Chunsen

"Warren DeLano warren:_:delsci.com" <owner-chemistry .. ccl.net> дµÀ£º

Sent to CCL by: "Warren DeLano" [warren|,|delsci.com]

Not sure, but PyMOL can get close:

http://pymol.sf.net/pmimag/atomic.png

However, it does take a bit of tweaking:

set_color nitrogen, [0.6, 0.7, 1.0]
fragment arg
as spheres
bg white
show sticks
set sphere_scale, 0.2
set stick_radius, 0.08
set stick_color, grey30
label not hydro, elem
color grey90, elem c
set label_color, black
set antialias,3
set ray_trace_mode,1
viewport 400
zoom complete=1
ray

http://pymol.sf.net

open source code

some builds are free

> -----Original Message-----
> From: owner-chemistry-*-ccl.net [mailto:owner-chemistry-*-ccl.net]
> Sent: Tuesday, November 06, 2007 6:58 AM
> To: Warren DeLano
> Subject: CCL: looking for a software for displaying the
> molecular structures
>
>
> Sent to CCL by: "Chunsen Li" [chunsen_li!A!yahoo.com.cn]
> Hi ,
>
> I want know which software can display the molecular
> structures as shown in Figure 1 of Angew. Chem. Int. Ed.
> 2005, 44, 2939.
> The bond in the structure is shown as single line and the
> labels can be add in the center of the atoms freely. In
> addition, the atoms can be in different patterns and colors.
> The similar picture and be found from http://qc.physto.se/home.htm.
>
> Which software can do this? Is it free of charge?
>
> Thank you.
>
>
> Chunsen Li
> Center for Theoretical Chemistry, Department of Chemistry,
> Xiamen University, Xiamen, 361005, China.
> Tel.: 86-592-2180418 Fax: 86-592-2184708
> email: lics01]-[xmu.edu.cn chunsen_li]-[yahoo.com.cn 2007-10-30
>
>
>
> -= 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 look up the X-Original-From: line
> in the mail header.
> > >
>> > > Conferences:
> http://server.ccl.net/chemistry/announcements/conferences/
>
> Search Messages: http://www.ccl.net/htdig (login: ccl,
> Password: search)
> > >
> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
> -+-+-+-+-+
>
>
>
>
>
>
>


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----------------------------------------
Chunsen Li
Center for Theoretical Chemistry, Department of Chemistry,
Xiamen University, Xiamen, 361005, China.
Tel.: 86-592-2180418 Fax: 86-592-2184708
email: lics01 .. xmu.edu.cn chunsen_li .. yahoo.com.cn

ÑÅ»¢ÓÊÏ䣬ÖÕÉú»ï°é£¡ --0-891977616-1194639644=:37343-- From owner-chemistry@ccl.net Fri Nov 9 22:13:00 2007 From: "Geoffrey Hutchison geoffh:pitt.edu" To: CCL Subject: CCL: Looking for program similar to AOMIX Message-Id: <-35578-071109200625-14500-Gs02Pu6aVkGz2IDVRHJkRg^_^server.ccl.net> X-Original-From: Geoffrey Hutchison Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Fri, 9 Nov 2007 19:36:54 -0500 Mime-Version: 1.0 (Apple Message framework v912) Sent to CCL by: Geoffrey Hutchison [geoffh:+:pitt.edu] > I am looking for software can do the functions of AOMIX, any help > welcome. > AOMIX site www.sg-chem.net. QMForge: http://qmforge.sourceforge.net/ This was recently announced on CCL.net a few days ago, actually. Cheers, -Geoff ------------------------------------------- Geoff Hutchison Assistant Professor University of Pittsburgh, Department of Chemistry 219 Parkman Avenue Pittsburgh, PA 15260