From owner-chemistry@ccl.net Thu Nov 5 04:59:01 2009 From: "laura S slaurami(a)yahoo.com" To: CCL Subject: CCL: Homology modeling and loop refinement Message-Id: <-40611-091105044834-2669-VWstJOGad5QzTdZFo7RUmQ-#-server.ccl.net> X-Original-From: laura S Content-Type: multipart/alternative; boundary="0-205789648-1257410899=:31501" Date: Thu, 5 Nov 2009 00:48:19 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: laura S [slaurami.:.yahoo.com] --0-205789648-1257410899=:31501 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hello!=0A=0AYou can try also the SWISS-MODEL server.=0A=0Ahttp://swissmodel= .expasy.org/=0Ahttp://swissmodel.expasy.org/workspace/index.php?func=3Dmode= lling_simple1=0A=0A =0AAmalia-Laura Seff =0A-------------------------------= -----------------=0APhD student=0ABabes-Bolyai University=0A=0AFaculty of C= hemistry and Chemical Engineering =0AInorganic Chemistry Department=0AMolec= ular Modeling Laboratory 101=0A =0AAdress: Arany J=E1nos Str. no. 11=0A = Ro - 400028, Cluj-Napoca, Romania=0A=0Atel: 40-724752988=0Afax: 40-= 264-590818=0A =0A=0A=0A=0A=0A________________________________=0AFrom: Werne= r K werner.schroedinger-x-googlemail.com =0ATo: "S= eff, Amalia Laura " =0ASent: Wed, November 4, 2= 009 6:52:41 PM=0ASubject: CCL: Homology modeling and loop refinement=0A=0A= =0ASent to CCL by: "Werner K" [werner.schroedinger^-^googlemail.com]=0AHi,= =0A=0Awhat are in your opinion the best softwares, free and commercial, for= protein homology modeling and loop refinement?=0A=0AThanks=0A=0AWS=0A=0A= =0A=0A-=3D This is automatically added to each message by the mailing scrip= t =3D-=0ATo recover the email address of the author of the message, please = change=0A= =0A=0A=0AE-mail to sub= scribers: CHEMISTRY+*+ccl.net or use:=0A http://www.ccl.net/cgi-bin/ccl/= send_ccl_message=0A=0AE-mail to administrators: CHEMISTRY-REQUEST+*+ccl.net o= r use=0A=0A=0ASubscrib= e/Unsubscribe: =0A=0A=0AB= efore posting, check wait time at: http://www.ccl.net=0A=0AJob: http://www.= ccl.net/jobs =0AConferences: http://server.ccl.net/chemistry/announcements/= conferences/=0A=0ASearch Messages: http://www.ccl.net/chemistry/searchccl/i= ndex.shtml=0A=0A=0A ==0A=0ARTFI: http://www.ccl.net/chemistry= /aboutccl/instructions/=0A=0A=0A --0-205789648-1257410899=:31501 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Hello!

You can try also the SWISS-MODEL server.

= http://sw= issmodel.expasy.org/
http:= //swissmodel.expasy.org/workspace/index.php?func=3Dmodelling_simple1
 
Amalia-Laura Seff
--= ----------------------------------------------
PhD student
Babes-Bolyai University
Faculty of Chemistry and C= hemical Engineering
Inorgani= c Chemistry Department
Molecular Modelin= g Laboratory 101
 
<= div>Adress: Arany J=E1nos Str. no. 11
   =          Ro - 400028, Cluj-Napoca, = Romania
tel: 40-724752988
fax= : 40-264-590818
 


From: Werner K werner.schroedinger-x-googlemail.com <ow= ner-chemistry+*+ccl.net>
To: "Seff, Amalia Laura " <slaurami+*+yahoo.com>
Sent: Wed, November 4, 2009 6:52:4= 1 PM
Subject: CCL: Homol= ogy modeling and loop refinement

=0A
Sent to CCL by: "Wern= er  K" [werner.schroedinger^-^googlemail.com]
Hi,

what are i= n your opinion the best softwares, free and commercial, for protein homolog= y modeling and loop refinement?

Thanks

WS



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=0A=0A
=0A=0A --0-205789648-1257410899=:31501-- From owner-chemistry@ccl.net Thu Nov 5 10:14:00 2009 From: "Sarah Ann Kebbell sarah.kebbell2_-_mail.dcu.ie" To: CCL Subject: CCL: Level of Theory for zwitterionic species Message-Id: <-40612-091105101110-23014-x79Shsx3s/vXY0mgLfzaIQ{}server.ccl.net> X-Original-From: "Sarah Ann Kebbell" Date: Thu, 5 Nov 2009 10:11:06 -0500 Sent to CCL by: "Sarah Ann Kebbell" [sarah.kebbell2^-^mail.dcu.ie] Dear CCLers, just wondering if anybody has an previous experience in locating intermediates that are zwitterionic in nature and if so, is B3LYP/6-31G(d) a sufficient level of theory to locate zwitterions at or do I need to change the theory/basis set to do so? Many thanks, Sarah From owner-chemistry@ccl.net Thu Nov 5 12:02:01 2009 From: "vadicherla tati reddy tatireddy.vadicherla#%#gmail.com" To: CCL Subject: CCL: Homology modeling and loop refinement Message-Id: <-40613-091105115453-11138-wORMidbOg89x68GKgoWrKw- -server.ccl.net> X-Original-From: vadicherla tati reddy Content-Type: multipart/alternative; boundary=0016e6435264e436680477a2253e Date: Thu, 5 Nov 2009 21:53:30 +0530 MIME-Version: 1.0 Sent to CCL by: vadicherla tati reddy [tatireddy.vadicherla,+,gmail.com] --0016e6435264e436680477a2253e Content-Type: text/plain; charset=ISO-8859-1 Hi..., You can try with PRIME (SCHRODINGER tool) for homology Modeling. Thanks Tati On Wed, Nov 4, 2009 at 10:22 PM, Werner K werner.schroedinger-x-googlemail.com wrote: > > Sent to CCL by: "Werner K" [werner.schroedinger^-^googlemail.com] > Hi, > > what are in your opinion the best softwares, free and commercial, for > protein homology modeling and loop refinement? > > Thanks > > WS> > > --0016e6435264e436680477a2253e Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi...,
You can try with PRIME (SCHRODINGER tool) for homology Modeling.<= br>
Thanks
Tati

On Wed, Nov 4, 2009= at 10:22 PM, Werner K werner.schroedinger-x-googlemail.com <owner-chemistry[]ccl.net> = wrote:

Sent to CCL by: "Werner =A0K" [werner.schroedinger^-^googlemail.com]
Hi,

what are in your opinion the best softwares, free and commercial, for prote= in homology modeling and loop refinement?

Thanks

WS

--0016e6435264e436680477a2253e-- From owner-chemistry@ccl.net Thu Nov 5 12:36:01 2009 From: "Tanja van Mourik tanja.vanmourik_._st-andrews.ac.uk" To: CCL Subject: CCL: Level of Theory for zwitterionic species Message-Id: <-40614-091105121753-18925-OTHfpc18JIMSvql3MpGjaw:server.ccl.net> X-Original-From: Tanja van Mourik Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 05 Nov 2009 16:47:35 +0000 MIME-Version: 1.0 Sent to CCL by: Tanja van Mourik [tanja.vanmourik * st-andrews.ac.uk] Dear Sarah, > > just wondering if anybody has an previous experience in locating intermediates that are zwitterionic in nature and if so, is B3LYP/6-31G(d) a sufficient level of theory to locate zwitterions at or do I need to change the theory/basis set to do so? > Zwitterions tend not to be stable in the gas phase. You'll need to use a solvent model, either a continuum solvation model like SCRF, or you can add explicit water molecules (or a combination of both approaches). Best wishes, Tanja -- ================================================================ Tanja van Mourik Senior Lecturer in Chemistry School of Chemistry, University of St. Andrews North Haugh, St. Andrews, Fife KY16 9ST, Scotland (UK) email: tanja.vanmourik#%#st-andrews.ac.uk web: http://chemistry.st-and.ac.uk/staffmember.php?id=tvm The University of St Andrews is a charity registered in Scotland: No SC013532 ================================================================ From owner-chemistry@ccl.net Thu Nov 5 13:49:00 2009 From: "=?ISO-8859-1?Q?Ulf_Ekstr=F6m?= ulfek^few.vu.nl" To: CCL Subject: CCL: Is there a reference DFT functional database? Message-Id: <-40615-091105094518-20376-71pBc8waJF0SEQ7Ti0qHOg]~[server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Ulf_Ekstr=F6m?= Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 5 Nov 2009 14:40:40 +0100 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Ulf_Ekstr=F6m?= [ulfek++few.vu.nl] Dear all, I am reimplementing some common DFT functionals and I wonder if there exists a reference database with "correct results" somewhere? In particular I am looking for values for the exchange correlation energy density at individual points, for example LYP at rho_a =3D 1, rho_b =3D 2, etc. I am not looking for energies for actual molecules. Regards, Ulf Ekstr=F6m, VU University Amsterdam From owner-chemistry@ccl.net Thu Nov 5 17:47:01 2009 From: "timothy lillestolen tlillest*_*gmail.com" To: CCL Subject: CCL: Is there a reference DFT functional database? Message-Id: <-40616-091105150946-24373-WvU0MWGFuj6hEc4olx/+dA-x-server.ccl.net> X-Original-From: timothy lillestolen Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; format=flowed; delsp=yes Date: Thu, 5 Nov 2009 20:09:27 +0000 Mime-Version: 1.0 (Apple Message framework v936) Sent to CCL by: timothy lillestolen [tlillest,,gmail.com] Dear Ulf, You could have a look at: http://www.cse.scitech.ac.uk/ccg/dft/ specifically the pointwise reference data. cheers, TIm Lillestolen University of Nottingham On 5 Nov 2009, at 13:40, Ulf Ekstr=F6m ulfek^few.vu.nl wrote: > > Sent to CCL by: =3D?ISO-8859-1?Q?Ulf_Ekstr=F6m? [ulfek++few.vu.nl] > Dear all, I am reimplementing some common DFT functionals and > I wonder if there exists a reference database with "correct results" > somewhere? In particular I am looking for values for the exchange > correlation energy density at individual points, for example LYP at > rho_a =3D 1, rho_b =3D 2, etc. I am not looking for energies for = actual > molecules. > > Regards, > Ulf Ekstr=F6m, VU University Amsterdam > > > > - This is automatically added to each message by the mailing script =3D-= > To recover the email address of the author of the message, please =20 > change> Conferences: http://server.ccl.net/chemistry/announcements/=20 > conferences/> > From owner-chemistry@ccl.net Thu Nov 5 20:38:01 2009 From: "Jonas Baltrusaitis jasius_1||yahoo.com" To: CCL Subject: CCL: using TINKER Message-Id: <-40617-091105203637-3846-NoDD88GCudcgXK0JRFA7Pg||server.ccl.net> X-Original-From: "Jonas Baltrusaitis" Date: Thu, 5 Nov 2009 20:36:34 -0500 Sent to CCL by: "Jonas Baltrusaitis" [jasius_1_-_yahoo.com] Dear all, is anybody using TINKER by any chance? I have been trying to run jobs using FFE but found it impossible. Manual is to concise and I can;t run any jobs as I find pdbxyz, nucleic and protein commands only, whereas in the manual it clearly shows Optimize, no idea how to get there. is there any mailing list or board for Tinker? thanks Jonas From owner-chemistry@ccl.net Thu Nov 5 21:13:01 2009 From: "Reinaldo Pis Diez reinaldo.pisdiez!=!gmail.com" To: CCL Subject: CCL: Is there a reference DFT functional database? Message-Id: <-40618-091105203328-3471-XaFf6Z8WQoRk3hqJkLYt4w .. server.ccl.net> X-Original-From: Reinaldo Pis Diez Content-Type: multipart/alternative; boundary=001636d34be93075ba0477a90b21 Date: Thu, 5 Nov 2009 21:37:07 -0300 MIME-Version: 1.0 Sent to CCL by: Reinaldo Pis Diez [reinaldo.pisdiez[#]gmail.com] --001636d34be93075ba0477a90b21 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Ulf, Have a look at http://www.cse.scitech.ac.uk/ccg/dft/contents.html. You'll find several atomic values (total energies, they are not partitioned into x and c contributions) and fortran subroutines implementing various functionals that could be useful for your purposes. Hope this helps. Regards, Reinaldo 2009/11/5 Ulf Ekstr=F6m ulfek^few.vu.nl > > Sent to CCL by: ?ISO-8859-1?Q?Ulf_Ekstr=F6m? [ulfek++few.vu.nl] > Dear all, I am reimplementing some common DFT functionals and > I wonder if there exists a reference database with "correct results" > somewhere? In particular I am looking for values for the exchange > correlation energy density at individual points, for example LYP at > rho_a =3D 1, rho_b =3D 2, etc. I am not looking for energies for actual > molecules. > > Regards, > Ulf Ekstr=F6m, VU University Amsterdam > > > > - This is automatically added to each message by the mailing script -> > > --001636d34be93075ba0477a90b21 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Ulf,

Have a look at http://www.cse.scitech.ac.uk/ccg/dft/contents.html.= You'll find several atomic values (total energies, they are not partit= ioned into x and c contributions) and fortran subroutines implementing vari= ous functionals that could be useful for your purposes.
Hope this helps.
Regards,

Reinaldo

2009/11/5 Ulf Ekstr=F6m ulfek^few.vu.nl <owner-ch= emistry!=!ccl.net>

Sent to CCL by: ?ISO-8859-1?Q?Ulf_Ekstr=F6m? [ulfek++few.vu.nl]
Dear all, I am reimplementing some common DFT functionals and
I wonder if there exists a reference database with "correct results&qu= ot;
somewhere? In particular I am looking for values for the exchange
correlation energy density at individual points, for example LYP at
rho_a =3D 1, rho_b =3D 2, etc. I am not looking for energies for actual
molecules.

Regards,
Ulf Ekstr=F6m, VU University Amsterdam



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--001636d34be93075ba0477a90b21-- From owner-chemistry@ccl.net Thu Nov 5 23:08:00 2009 From: "A VM fray.gory###gmail.com" To: CCL Subject: CCL: using TINKER Message-Id: <-40619-091105230629-7229-vz28mc8t3INLdLqPHTa/4w^server.ccl.net> X-Original-From: A VM Content-Type: multipart/alternative; boundary=00504501764b434f540477abf746 Date: Thu, 5 Nov 2009 23:06:18 -0500 MIME-Version: 1.0 Sent to CCL by: A VM [fray.gory{}gmail.com] --00504501764b434f540477abf746 Content-Type: text/plain; charset=ISO-8859-1 Dear Jonas, For linux... To me the greatest trick resides in defining correctly the PATH variable in the shell that you are using. (I mean, in my case, PATH=/opt/MolecularStructure/tinker/bin:$PATH) Also, as I work is generating the coordinates files with MOLDEN, and assigning carefully the parameters with the 'FF' in the control window, see MOLDEN web page, and saving them as TINKER xyz. Hope that it helps (at least a little bit). Alvaro Alvaro Vazquez-Mayagoitia On Thu, Nov 5, 2009 at 8:36 PM, Jonas Baltrusaitis jasius_1||yahoo.com < owner-chemistry]|[ccl.net> wrote: > > Sent to CCL by: "Jonas Baltrusaitis" [jasius_1_-_yahoo.com] > Dear all, > > is anybody using TINKER by any chance? I have been trying to run jobs using > FFE but found it impossible. Manual is to concise and I can;t run any jobs > as I find pdbxyz, nucleic and protein commands only, whereas in the manual > it clearly shows Optimize, no idea how to get there. > > is there any mailing list or board for Tinker? > > thanks > > Jonas> > > --00504501764b434f540477abf746 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Jonas,

For linux...

To me the greatest trick resides= in defining correctly the PATH variable
in the shell that you are using= .
(I mean, in my case, PATH=3D/opt/MolecularStructure/tinker/bin:$PATH)<= br>
Also, as I work is generating the coordinates files with MOLDEN, and=A0=
assigning carefully the parameters with the 'FF' in the control= window,
see MOLDEN web page, and saving them as TINKER xyz.

Hope= that it helps (at least a little bit).

Alvaro



Alvaro Vazquez-Mayagoitia
<= br>

On Thu, Nov 5, 2009 at 8:36 PM, Jonas= Baltrusaitis jasius_1||yaho= o.com <owner-chemistry]|[ccl.net> wrote:

Sent to CCL by: "Jonas =A0Baltrusaitis" [jasius_1_-_yahoo.com]
Dear all,

is anybody using TINKER by any chance? I have been trying to run jobs using= FFE but found it impossible. Manual is to concise and I can;t run any jobs= as I find pdbxyz, nucleic and protein commands only, whereas in the manual= it clearly shows Optimize, no idea how to get there.

is there any mailing list or board for Tinker?

thanks

Jonas



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--00504501764b434f540477abf746--