From owner-chemistry@ccl.net Fri May 25 04:28:01 2007 From: "andrea spitaleri spitaleri.andrea!=!hsr.it" To: CCL Subject: CCL: HADDOCK installation Message-Id: <-34347-070525042641-2127-tPxz/Rzf5XEdC2jGLI5gEw!=!server.ccl.net> X-Original-From: andrea spitaleri Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 25 May 2007 10:26:11 +0200 MIME-Version: 1.0 Sent to CCL by: andrea spitaleri [spitaleri.andrea###hsr.it] Hi, > 1. what is the significance of ARIA, should we install ARIA to run haddock. ARIA is another software developed by Prof. M. Nilges. It is used to calculate protein nmr structure using nmr data. It is bases on CNS too. So to run HADDOCK you do not need to install ARIA. HADDOCK, developed by Prof. A. Bonvin, is based on the ARIA's idea. > 2. i learn that run.CNS is the file where we have make the changes to > run haddock and should execute that file, but where should we execute > it, is it in python, CNS or haddock directories.... Once you have created the run1 project dir, you have to edit run.cns in run1 and in run1 dir you have to type "haddock", which will take care of everything. Be aware about the queue issue in the run.cns (read the FAQ in HADDOCK webpage) > 3. in this process of installation i didn't give the path of python, > where should we give that. In principle you need to edit only the haddock_configure.csh and set up the correct dir of haddock in. For instance I have: setenv HADDOCK /usr/local/haddock2.0_devel By the way, Prof. Bonvin has released the new version of haddock, HADDOCK-2.0, which can be used under request to him. Just follow the instruction in the webpage of HADDOCK. Please let me know if you need more help, Regards andrea -- ------------------------------- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom/ ------------------------------- ******************************************************************** Sostieni la ricerca del San Raffaele con il 5permille! E' SEMPLICE E NON COSTA NULLA. Basta indicare nell'apposito riquadro della dichiarazione dei redditi ("Ricerca sanitaria") il codice fiscale della Fondazione Centro S. Raffaele del Monte Tabor: 03 06 42 80 153 e ricordarsi di firmare. Se vuoi saperne di piu' scrivi a 5permille|-|hsr.it o vai sul sito www.5xmille.org From owner-chemistry@ccl.net Fri May 25 08:29:00 2007 From: "San-Fabian Emilio sanfa%ua.es" To: CCL Subject: CCL: DFT-HF theories Message-Id: <-34348-070525060918-31771-TCelyapydOBQGI0wwgewmw*o*server.ccl.net> X-Original-From: "San-Fabian Emilio" Date: Fri, 25 May 2007 06:09:14 -0400 Sent to CCL by: "San-Fabian Emilio" [sanfa^ua.es] I'm looking for a paper or book with the expression of the derivate the Hartree-Fock exchange energy in respect to the density. Any suggestions will be greatly appreciated. From owner-chemistry@ccl.net Fri May 25 09:54:00 2007 From: "David Reichert ReichertD**mir.wustl.edu" To: CCL Subject: CCL: condensed fukui indices Message-Id: <-34349-070524180127-22268-JulwBGzs4E1ASkLE0T+sNw:-:server.ccl.net> X-Original-From: David Reichert Content-Disposition: inline Content-type: multipart/alternative; Boundary="0__=09BBF876DFE024168f9e8a93df938690918c09BBF876DFE02416" Date: Thu, 24 May 2007 16:15:43 -0500 MIME-Version: 1.0 Sent to CCL by: David Reichert [ReichertD^^mir.wustl.edu] --0__=09BBF876DFE024168f9e8a93df938690918c09BBF876DFE02416 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: quoted-printable Hi all, I'm trying to get a handle on calculating condensed fukui indices follo= wing the method of Wang and Mortier (JACS 108(19) 1986 5708-5711) and am completely unable to reproduce any literature results. For example following Arulmozhiraja and Kolandaivel (Molec. Physics 90(1) 1997 55-6= 2) they report indices for BH2F from HF/6-311G* calculations using Mullike= n charges and Natural Population Analysis charges, when I try to repeat t= hese I get nothing close. Does anyone have a reliable procedure, and or tips= on doing this types of analysis? My neutral charges appear to match well t= o literature values so I figure I must be going wrong with the N-1 and N+= 1 calculations, but at this point I can't figure out what I'm doing wrong= . thanks, -david David Reichert, Ph.D. Asst. Professor Radiology Washington University School of Medicine 510 S. Kingshighway, Campus Box 8225 St Louis, MO 63110 e-mail: reichertd===wustl.edu http://scoobie.wustl.edu/ voice: (314) 362-8461 fax: (314) 362-9940= --0__=09BBF876DFE024168f9e8a93df938690918c09BBF876DFE02416 Content-type: text/html; charset=US-ASCII Content-Disposition: inline Content-transfer-encoding: quoted-printable

Hi all,
I'm trying to get a handle on calculating condensed fukui indices follo= wing the method of Wang and Mortier (JACS 108(19) 1986 5708-5711) and a= m completely unable to reproduce any literature results. For example fo= llowing Arulmozhiraja and Kolandaivel (Molec. Physics 90(1) 1997 55-62)= they report indices for BH2F from HF/6-311G* calculations using Mullik= en charges and Natural Population Analysis charges, when I try to repea= t these I get nothing close. Does anyone have a reliable procedure, and= or tips on doing this types of analysis? My neutral charges appear to = match well to literature values so I figure I must be going wrong with = the N-1 and N+1 calculations, but at this point I can't figure out what= I'm doing wrong.
thanks,
-david
David Reichert, Ph.D.
Asst. Professor Radiology
Washington University School of Medicine
510 S. Kingshighway, Campus Box 8225
St Louis, MO 63110

e-mail: reichertd===wustl.edu
http://scoobie.wustl.edu/
=
voice: (314) 362-8461
fax: (314) 362-9940= --0__=09BBF876DFE024168f9e8a93df938690918c09BBF876DFE02416-- From owner-chemistry@ccl.net Fri May 25 10:29:01 2007 From: "Yubo Fan yubofan(0)mail.chem.tamu.edu" To: CCL Subject: CCL: show ruler in VMD Message-Id: <-34350-070525101808-10652-dttFXCZCQ7JFRv3q5So+OA###server.ccl.net> X-Original-From: "Yubo Fan" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0009_01C79EAD.85A76760" Date: Fri, 25 May 2007 09:17:31 -0500 MIME-Version: 1.0 Sent to CCL by: "Yubo Fan" [yubofan+/-mail.chem.tamu.edu] This is a multi-part message in MIME format. ------=_NextPart_000_0009_01C79EAD.85A76760 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello, A quick question about VMD. Is there any way to show ruler (ie angstroms = in unit) in VMD window? Thanks, Yubo =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Dr. Yubo Fan Email: yubofan() mail.chem.tamu.edu Department of Chemistry Tel: 1-979-845-5237 Texas A&M University College Station, TX 77843 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D ------=_NextPart_000_0009_01C79EAD.85A76760 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Hello,
 
A quick question about VMD. Is there = any way to=20 show ruler (ie angstroms in unit) in VMD window?
 
Thanks,
 
Yubo
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Dr. Yubo=20 Fan           &nbs= p;  =20 Email: yubofan() mail.chem.tamu.edu=
Department=20 of Chemistry    Tel:   1-979-845-5237
Texas = A&M=20 University
College Station, TX=20 77843
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
------=_NextPart_000_0009_01C79EAD.85A76760-- From owner-chemistry@ccl.net Fri May 25 11:04:00 2007 From: "James Robinson James.Robinson]^[prosonix.co.uk" To: CCL Subject: CCL: DFT-HF theories Message-Id: <-34351-070525103223-18687-JOz924HG+FT3IRQNX5aRoA/a\server.ccl.net> X-Original-From: "James Robinson" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 25 May 2007 15:27:07 +0100 MIME-Version: 1.0 Sent to CCL by: "James Robinson" [James.Robinson^_^prosonix.co.uk] Szabo and Ostlund, modern quantum chemistry, Dover publications - first choice.. See also; An experimental chemist's guide to ab initio quantum chemistry Jack Simons J. Phys. Chem.; 1991; 95(3) pp 1017 - 1029; DOI: 10.1021/j100156a002 There is also a good read by P.D Offenhartz, can't remember the title but is an ace read, just like that book by C.W.N Cumper - wave mechanics for Chemists - can't get those two books for love or money it seems. Could I bribe anyone on the list? james -----Original Message----- > From: owner-chemistry-.-ccl.net [mailto:owner-chemistry-.-ccl.net] Sent: 25 May 2007 11:09 To: James Robinson Subject: CCL: DFT-HF theories Sent to CCL by: "San-Fabian Emilio" [sanfa^ua.es] I'm looking for a paper or book with the expression of the derivate the Hartree-Fock exchange energy in respect to the density. Any suggestions will be greatly appreciated.http://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 Fri May 25 12:32:01 2007 From: "chupvl chupvl###gmail.com" To: CCL Subject: CCL: Pharmacophore modeling Message-Id: <-34352-070525122226-11970-Vj2MaYDSxCq7XZsOMHmBxg..server.ccl.net> X-Original-From: chupvl Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 25 May 2007 19:51:27 +0400 MIME-Version: 1.0 Sent to CCL by: chupvl [chupvl ~~ gmail.com] Hi, There is no free pharmacophore modeling software, but for pharmacophore based virtual screening there is one 3DFS - very simple algo, but very unreliable results. Vladimir Chupakhin Richard L Wood rwoodphd[A]msn.com wrote: > Sent to CCL by: "Richard L Wood" [rwoodphd=msn.com] > Hi all, > > Do any of you know of any FREE programs to do pharmacophore modeling that wil run under Windows? I'm currently using Sybyl under Linux, but I'd like to try something else. If not Windows, Linux would be alright, but I'd prefer that it run under Windows. > > The bottom line is that it must be free. > > Richard> > > > > From owner-chemistry@ccl.net Fri May 25 23:50:01 2007 From: "Kalyan chaitanya kalyanpulipaka+/-gmail.com" To: CCL Subject: CCL: HADDOCK installation Message-Id: <-34353-070525233939-13707-IZKjPV3rz2DzjcaaJQJZWA]*[server.ccl.net> X-Original-From: "Kalyan chaitanya" Content-Type: multipart/alternative; boundary="----=_Part_113529_407266.1180150758257" Date: Sat, 26 May 2007 09:09:18 +0530 MIME-Version: 1.0 Sent to CCL by: "Kalyan chaitanya" [kalyanpulipaka===gmail.com] ------=_Part_113529_407266.1180150758257 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi Andrea, Thank you very much for all ur responses, believe me they are indeed very helpful for me in understanding HADDOCK, i know you don't have to do all this and it is only out of ur intrest that u took time in responding me.....once agian thank you very much, with infromation u have given me i'll try to work HADDOCK and communicate you. Regards, P.Kalyan On 5/25/07, andrea spitaleri spitaleri.andrea!=!hsr.it < owner-chemistry!^!ccl.net> wrote: > > > Sent to CCL by: andrea spitaleri [spitaleri.andrea###hsr.it] > Hi, > > > 1. what is the significance of ARIA, should we install ARIA to run > haddock. > > ARIA is another software developed by Prof. M. Nilges. It is used to > calculate protein nmr structure > using nmr data. It is bases on CNS too. So to run HADDOCK you do not need > to install ARIA. HADDOCK, > developed by Prof. A. Bonvin, is based on the ARIA's idea. > > > 2. i learn that run.CNS is the file where we have make the changes to > > run haddock and should execute that file, but where should we execute > > it, is it in python, CNS or haddock directories.... > > Once you have created the run1 project dir, you have to edit run.cns in > run1 and in run1 dir you > have to type "haddock", which will take care of everything. Be aware about > the queue issue in the > run.cns (read the FAQ in HADDOCK webpage) > > > 3. in this process of installation i didn't give the path of python, > > where should we give that. > > In principle you need to edit only the haddock_configure.csh and set up > the correct dir of haddock > in. For instance I have: > > setenv HADDOCK /usr/local/haddock2.0_devel > > By the way, Prof. Bonvin has released the new version of haddock, > HADDOCK-2.0, which can be used > under request to him. Just follow the instruction in the webpage of > HADDOCK. > > Please let me know if you need more help, > > Regards > > andrea > > > > -- > ------------------------------- > Andrea Spitaleri PhD > Dulbecco Telethon Institute > c/o DIBIT Scientific Institute > Biomolecular NMR, 1B4 > Via Olgettina 58 > 20132 Milano (Italy) > http://biomolecularnmr.ihsr.dom/ > ------------------------------- > > ******************************************************************** > Sostieni la ricerca del San Raffaele con il 5permille! > E' SEMPLICE E NON COSTA NULLA. > Basta indicare nell'apposito riquadro della dichiarazione dei > redditi ("Ricerca sanitaria") > il codice fiscale della > Fondazione Centro S. Raffaele del Monte Tabor: > 03 06 42 80 153 e ricordarsi di firmare. > Se vuoi saperne di piu' scrivi a 5permille() hsr.it o vai sul sito > www.5xmille.org> > > > ------=_Part_113529_407266.1180150758257 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Hi Andrea,
 
Thank you very much for all ur responses, believe me they are indeed very helpful for me in understanding HADDOCK, i know you don't have to do all this and it is only out of ur intrest that u took time in responding me.....once agian thank you very much,
with infromation u have given me i'll try to work HADDOCK and communicate you.
 
Regards,
 
P.Kalyan

 
On 5/25/07, andrea spitaleri spitaleri.andrea!=!hsr.it <owner-chemistry!^!ccl.net> wrote:

Sent to CCL by: andrea spitaleri [spitaleri.andrea###hsr.it]
Hi,

> 1. what is the significance of ARIA, should we install ARIA to run haddock.

ARIA is another software developed by Prof. M. Nilges. It is used to calculate protein nmr structure
using nmr data. It is bases on CNS too. So to run HADDOCK you do not need to install ARIA. HADDOCK,
developed by Prof. A. Bonvin, is based on the ARIA's idea.

> 2. i learn that run.CNS is the file where we have make the changes to
> run haddock and should execute that file, but where should we execute
> it, is it in python, CNS or haddock directories....

Once you have created the run1 project dir, you have to edit run.cns in run1 and in run1 dir you
have to type "haddock", which will take care of everything. Be aware about the queue issue in the
run.cns (read the FAQ in HADDOCK webpage)

> 3. in this process of installation i didn't give the path of python,
> where should we give that.

In principle you need to edit only the haddock_configure.csh and set up the correct dir of haddock
in. For instance I have:

setenv HADDOCK /usr/local/haddock2.0_devel

By the way, Prof. Bonvin has released the new version of haddock, HADDOCK-2.0, which can be used
under request to him. Just follow the instruction in the webpage of HADDOCK.

Please let me know if you need more help,

Regards

andrea



--
-------------------------------
Andrea Spitaleri PhD
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
http://biomolecularnmr.ihsr.dom/
-------------------------------

********************************************************************
Sostieni la ricerca del San Raffaele con il 5permille!
E' SEMPLICE E NON COSTA NULLA.
Basta indicare nell'apposito riquadro della dichiarazione dei
redditi ("Ricerca sanitaria")
il codice fiscale della
Fondazione Centro S. Raffaele del Monte Tabor:
03 06 42 80 153 e ricordarsi di firmare.
Se vuoi saperne di piu' scrivi a 5permille() hsr.it o vai sul sito
www.5xmille.org



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