From owner-chemistry@ccl.net Wed Feb 6 09:00:00 2008 From: "Pieter Stouten Pieter.Stouten(0)glpg.com" To: CCL Subject: CCL: What happened to the docking program Flo-QXP ? Message-Id: <-36235-080206085846-8188-kUjoudttEmk+X+bA2nIG6A\a/server.ccl.net> X-Original-From: "Pieter Stouten" Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C868C8.C4B537A8" Date: Wed, 6 Feb 2008 15:01:30 +0100 MIME-Version: 1.0 Sent to CCL by: "Pieter Stouten" [Pieter.Stouten::glpg.com] This is a multi-part message in MIME format. ------_=_NextPart_001_01C868C8.C4B537A8 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Thistlesoft is Colin's company (he is from Scotland; Thistle is the national emblem of Scotland). His is a one-man enterprise. Colin is keenly interested in developing high-quality scientific tools, but does not like to be distracted by mundane issues such as selling his software. =20 At my previous job, we used QXP with quite a bit of success: we were one of those groups of geeks that compared docking programs (well actually, we had experts run the programs to get a fair comparison) and QXP came out best. We did not test Glide though. I don't know anything about the current status of QXP, but you might try to contact Colin at cmcma ^_^ ix.netcom.com. If that does not work, you can contact Jean-Yves Trosset . Jean-Yves is a QXP guru, who is in regular contact with Colin and who is also available to do QXP consulting (or carry out the job for you if so desired). =20 Hope this helps, =20 Pieter =20 Pieter Stouten Group Leader Computational Chemistry Galapagos, Mechelen, Belgium -----Original Message----- > From: owner-chemistry/./ccl.net [mailto:owner-chemistry/./ccl.net]=20 Sent: Tuesday, 05 February, 2008 20:28 PM To: Pieter Stouten Subject: CCL: What happened to the docking program Flo-QXP ? =20 =20 Sent to CCL by: "David P" [ccl_list^_^giantscience.com] Colin McMartin's program FLO-QXP has gotten a number of very positive mentions over the past few years in the various "we compare all the docking programs" surveys. However, as far as I can tell it is barely available, if at all. I've done as many smart Google searches as I can think of, and I come up pretty empty. Apparently, it used to be available from the link uwmml.pharmacy.wisc.edu/Flo/floindx.html, but that address is completely out of date/dead. Going to the U.Wisc website, I couldn't find an equivalent website. =20 Supposedly, the software is also sold through "Thistlesoft" software, but they don't have a website, if they actually still exist. =20 Does anyone know if this software is still being developed, and if so, > from where? =20 Is this software package still competitive with others? =20 =20 =20 -=3D This is automatically added to each message by the mailing script = =3D-=20http://www.ccl.net/cgi-bin/ccl/send_ccl_message =20=20 Subscribe/Unsubscribe:=20=20=20 Job: http://www.ccl.net/jobs=20=20=20http://www.ccl.net/spammers.txt =20=20 =20 --=0AThis e-mail and its attachment(s) (if any) may contain confidential and/= or proprietary information and is intended for its addressee(s) only. Any un= authorized use of the information contained herein (including, but not limit= ed to, alteration, reproduction, communication, distribution or any other fo= rm of dissemination) is strictly prohibited. If you are not the intended add= ressee, please notify the orginator promptly and delete this e-mail and its = attachment(s) (if any) subsequently. =0A=0AGalapagos nor any of its affiliates s= hall be liable for direct, special, indirect or consequential damages arisin= g from alteration of the contents of this message (by a third party) or as a= result of a virus being passed on.=0A=0A ------_=_NextPart_001_01C868C8.C4B537A8 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Thistlesoft is Colin's company (he is from = Scotland; Thistle is the national = emblem of Scotland). His is a one-man enterprise. Colin is keenly interested in developing = high-quality scientific tools, but does not like to be distracted by mundane issues = such as selling his software.

 

At my previous job, we used QXP with quite a bit of success: we were one of those groups of geeks that compared docking = programs (well actually, we had experts run the programs to get a fair = comparison) and QXP came out best. We did not test Glide though. I don't know anything = about the current status of QXP, but you might try to contact Colin at cmcma = ^_^ ix.netcom.com. If that does not work, you can contact Jean-Yves Trosset <jytrosset = ^_^ gmail.com>. Jean-Yves is a QXP guru, who is in regular contact with Colin and who is = also available to do QXP consulting (or carry out the job for you if so = desired).

 

Hope this helps,

 

Pieter

 

Pieter Stouten
Group Leader Computational Chemistry
Galapagos, = Mechelen, = Belgium

-----Original Message-----
> From: owner-chemistry/./ccl.net [mailto:owner-chemistry/./ccl.net]
Sent: Tuesday, 05 February, 2008 20:28 PM
To: Pieter Stouten
Subject: CCL: What happened to the docking program Flo-QXP = ?

 

 

Sent to CCL by: "David  P" [ccl_list^_^giantscience.com]

Colin McMartin's program FLO-QXP has gotten a = number of very positive mentions over the past few years in the various "we = compare all the docking programs" surveys. However, as far as I can tell it = is barely available, if at all. I've done as many smart Google searches as = I can think of, and I come up pretty empty. Apparently, it used to be = available from the link uwmml.pharmacy.wisc.edu/Flo/floindx.html, but that address is completely out of date/dead. Going to the U.Wisc website, I couldn't = find an equivalent website.

 

Supposedly, the software is also sold through "Thistlesoft" software, but they don't have a website, if they actually still exist.

 

Does anyone know if this software is still being developed, and if so, from where?

 

Is this software package still competitive with = others?

 

 

 

-=3D This is automatically added to each message by = the mailing script =3D-

To recover the email address of the author of the = message, please change

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=

This e-mail and its attachment(s) (if any) may contain confidential= and/or proprietary information and is intended for its addressee(s) only. A= ny unauthorized use of the information contained herein (including, but not = limited to, alteration, reproduction, communication, distribution or any oth= er form of dissemination) is strictly prohibited. If you are not the intende= d addressee, please notify the orginator promptly and delete this e-mail and= its attachment(s) (if any) subsequently. =0A=0AGalapagos nor any of its affilia= tes shall be liable for direct, special, indirect or consequential damages a= rising from alteration of the contents of this message (by a third party) or= as a result of a virus being passed on.=0A=0A
= ------_=_NextPart_001_01C868C8.C4B537A8-- From owner-chemistry@ccl.net Wed Feb 6 11:02:01 2008 From: "John Edward jeedward===yahoo.com" To: CCL Subject: CCL: Draft paper submission deadline is extended: BCBGC-08 Message-Id: <-36236-080206102311-3756-sQ1gGZRDdna0fQUEL9NfWg-x-server.ccl.net> X-Original-From: John Edward Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-720576307-1202311378=:53098" Date: Wed, 6 Feb 2008 07:22:58 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: John Edward [jeedward * yahoo.com] --0-720576307-1202311378=:53098 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear Professors, Colleagues and Friends Kindly share the announcement below with those who may be interested: thank you in advance. Sincerely John Edward BCBGC-08 Draft paper submission deadline is extended. The 2008 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-08) (website: www.PromoteResearch.org ) will be held during July 7-10 2008 in Orlando, FL, USA. The draft paper submission deadline is extended until February 19 2008 due to several requests from the authors. The conference will be held at the same time and location where several major events (see below) will be taking place. BCBGC brings together both academic and industrial scientists and developers from a diverse range of disciplines including bioinformatics, computer science, computational biology, genomics, proteomics and chemoinformatics. One of the main goals of the conference is to promote the dissemination of research to a multidisciplinary audience and to facilitate communication among researchers in different fields. Papers that demonstrate applications of existing techniques or developments of new methods are equally welcomed to the conference. Sincerely John Edward · International Conference on Artificial Intelligence and Pattern Recognition (AIPR-08) · International Conference on Automation, Robotics and Control Systems (ARCS-08) · International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-08) · International Conference on Enterprise Information Systems and Web Technologies (EISWT-08) · International Conference on High Performance Computing, Networking and Communication Systems (HPCNCS-08) · International Conference on Software Engineering Theory and Practice (SETP-08) · International Conference on Theoretical and Mathematical Foundations of Computer Science (TMFCS-08) --------------------------------- Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. --0-720576307-1202311378=:53098 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit 
Dear Professors, Colleagues and Friends
 
Kindly share the announcement below with those who may be interested: thank you in advance.  
 
Sincerely
John Edward
 
 
BCBGC-08 Draft paper submission deadline is extended.
 
The 2008 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-08) (website: www.PromoteResearch.org ) will be held during July 7-10 2008 in Orlando, FL, USA.  The draft paper submission deadline is extended until February 19 2008 due to several requests from the authors. The conference will be held at the same time and location where several major events (see below) will be taking place.
 
BCBGC brings together both academic and industrial scientists and developers from a diverse range of disciplines including bioinformatics, computer science, computational biology, genomics, proteomics and chemoinformatics. One of the main goals of the conference is to promote the dissemination of research to a multidisciplinary audience and to facilitate communication among researchers in different fields. Papers that demonstrate applications of existing techniques or developments of new methods are equally welcomed to the conference.
 
Sincerely
John Edward
 
·        International Conference on Artificial Intelligence and Pattern Recognition (AIPR-08)
·        International Conference on Automation, Robotics and Control Systems (ARCS-08)
·        International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-08)
·        International Conference on Enterprise Information Systems and Web Technologies (EISWT-08)
·        International Conference on High Performance Computing, Networking and Communication Systems (HPCNCS-08)
·        International Conference on Software Engineering Theory and Practice (SETP-08)  
·        International Conference on Theoretical and Mathematical Foundations of Computer Science (TMFCS-08)

Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. --0-720576307-1202311378=:53098-- From owner-chemistry@ccl.net Wed Feb 6 12:03:00 2008 From: "Bruno Andrade bandradefsa::yahoo.com.br" To: CCL Subject: CCL: Res: CCL: How to perform a protein MD in Gromacs, with solvent Message-Id: <-36237-080204140150-6289-jpOf5g7kpubsofrvT1EjdQ||server.ccl.net> X-Original-From: Bruno Andrade Content-Type: multipart/alternative; boundary="0-1147755742-1202148099=:17881" Date: Mon, 4 Feb 2008 10:01:39 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Bruno Andrade [bandradefsa%%yahoo.com.br] --0-1147755742-1202148099=:17881 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Yes, you're right!=0A=0AI will post to gmx list. I'm just getting the right= steps to perform a good MD, just begining.=0A=0AThank you very much, =0ABr= uno S. Andrade=0A =0APPGBIOTEC - Programa de P=C3=B3s-gradua=C3=A7=C3=A3o e= m Biotecnologia - UEFS/FIOCRUZ=0AGen=C3=B4mica e Prote=C3=B4mica de microrg= anismos / Modelagem Molecular=0ATels: (75)81075337 / (75)32248296=0AE-mails= : bandradefsa*o*yahoo.com.br / bandradefsa*o*gmail.com / b.andrade*o*uefs.br=0A = =0APPGBIOTEC - Graduate Program in Biotechnology=0AGenomics and Proteomics = of Microorganisms / Molecular Modeling=0APhones: +55(75)81075337 / 32248132= =0AFax: +55(75)32248132=0AEmails: bandradefsa*o*yahoo.com.br / bandradefsa*o*gm= ail.com / b.andrade*o*uefs.br=0A=0A=0A=0A----- Mensagem original ----=0ADe: L= =C3=A9on Salgado leon.salgado _ gmail.com =0APara:= "Andrade, Bruno Silva " =0AEnviadas: Seg= unda-feira, 4 de Fevereiro de 2008 9:33:00=0AAssunto: CCL: How to perform a= protein MD in Gromacs, with solvent=0A=0A=0ASent to CCL by: =3D?ISO-8859-1= ?Q?L=3DE9on_Salgado?=3D [leon.salgado:_:gmail.com]=0ABruno=0A=0AWhy don't y= ou post your question to gmx mailing list?=0AYou have there a big community= ready to help, including beginners. But =0Ahey, b4 asking something, searc= h mailing list first for similar doubts. =0AAnd above all, read the manual = and available tutorials.=0A=0AIf you are having crashes right from the begi= nning, then your system is =0Anot ready to be simulated ;-)=0ANever forget = that MD systems must be handled gently, starting by =0Aminimizing the solve= nt while restraining the protein, and later all the =0Asystem without coord= inate restraining. Next you need an equilibration b4 =0Amoving to the produ= ction run. Only then, you will be able to analyze =0Asolvent molecules near= the protein. But that's another story.=0A=0ACheers,=0AL.s.=0A=0A=0A=0ABrun= o Andrade bandradefsa/ayahoo.com.br wrote:=0A> Sent to CCL by: "Bruno Andr= ade" [bandradefsa-$-yahoo.com.br]=0A> Hi there,=0A>=0A> I'm currently using= gromacs program (as beginer), and I had some crashes in the calculations. = I am trying to perform a MD using water as solvent, but in gromacs I could = not found any option to use the solvent effect directly binded to the prote= in target, I just found the genbox option and using it, the program retuns = me a crash message (system colapses with box, or something like "your syste= m is probably not equilibrated").=0A>=0A> Ps.: The system converges on the = energy minimization, using option 6 force field. =0A>=0A> How can I perform= it better?=0A>=0A> Thank you for you help.=0A>=0A> Bruno Andrade.=0A>=0A>= =0A=0A=0A=0A-=3D This is automatically added to each message by the mailing= script =3D-=0ATo recover the email address of the author of the message, p= lease change=0Athe strange characters on the top line to the *o* sign. You ca= n also=0A=0A=0AE-mail = to subscribers: CHEMISTRY*o*ccl.net or use:=0A http://www.ccl.net/cgi-bi= n/ccl/send_ccl_message=0A=0AE-mail to administrators: CHEMISTRY-REQUEST*o*ccl= .net or use=0A=0A=0ASu= bscribe/Unsubscribe: =0A= =0A=0A=0A=0AJob: http= ://www.ccl.net/jobs =0AConferences: http://server.ccl.net/chemistry/announc= ements/conferences/=0A=0ASearch Messages: http://www.ccl.net/htdig (login:= ccl, Password: search)=0A=0AIf your mail bounces from CCL with 5.7.1 error= , check:=0A=0A=0ARTFI: http://www.ccl.= net/chemistry/aboutccl/instructions/=0A=0A=0A Abra sua conta no Yahoo!= Mail, o =C3=BAnico sem limite de espa=C3=A7o para armazenamento!=0Ahttp://= br.mail.yahoo.com/ --0-1147755742-1202148099=:17881 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
=0A
Yes, you're right!
=0A
 
=0AI will post to gmx list. I'm just getting the right steps to perform = a good MD, just begining.
=0A
 
=0A
Thank you very m= uch, 
Bruno S. Andrade=0A
=0A
 
=0A
P= PGBIOTEC - Programa de P=C3=B3s-gradua=C3=A7=C3=A3o em Biotecnologia - UEFS= /FIOCRUZ
Gen=C3=B4mica e Prote=C3=B4mica de microrganismos / Modelagem M= olecular
Tels: (75)81075337 / (75)32248296
E-mails: bandradefsa*o*yahoo= .com.br / bandradefsa*o*gmail.com / b.andrade*o*uefs.br
=0A
 =0A
PPGBIOTEC - Graduate Program in Biotechnology
Genomics and Pro= teomics of Microorganisms / Molecular Modeling
Phones: +55(75)81075337 /= 32248132
Fax: +55(75)32248132
Emails: bandradefsa*o*yahoo.com.br / ban= dradefsa*o*gmail.com / b.andrade*o*uefs.br=0A


=0A
----- Mensagem= original ----
De: L=C3=A9on Salgado leon.salgado _ gmail.com <owner-= chemistry*o*ccl.net>
Para: "Andrade, Bruno Silva " <bandrade= fsa*o*yahoo.com.br>
Enviadas: Segunda-feira, 4 de Fevereiro de 2008 9:3= 3:00
Assunto: CCL: How to perform a protein MD in Gromacs, with solvent<= BR>

Sent to CCL by: =3D?ISO-8859-1?Q?L=3DE9on_Salgado?=3D [leon.salg= ado:_:gmail.com]
Bruno

Why don't you post your question to gmx ma= iling list?
You have there a big community ready to help, including begi= nners. But
hey, b4 asking something, search mailing list first for simi= lar doubts.
And above all, read the manual and available tutorials.
=
If you are having crashes right from the beginning, then your system is=
not ready to be simulated ;-)
Never forget that MD systems must be = handled gently, starting by
minimizing the solvent while restraining the protein, and later all the
system without coordi= nate restraining. Next you need an equilibration b4
moving to the produ= ction run. Only then, you will be able to analyze
solvent molecules nea= r the protein. But that's another story.

Cheers,
L.s.


=
Bruno Andrade bandradefsa/ayahoo.com.br wrote:
> Sent to CCL by: = "Bruno  Andrade" [bandradefsa-$-yahoo.com.br]
> Hi there,
>= ;
> I'm currently using gromacs program (as beginer), and I had some = crashes in the calculations. I am trying to perform a MD using water as sol= vent, but in gromacs I could not found any option to use the solvent effect= directly binded to the protein target, I just found the genbox option and = using it, the program retuns me a crash message (system colapses with box, = or something like "your system is probably not equilibrated").
>
&= gt; Ps.: The system converges on the energy minimization, using option 6 force field.
>
> How can I perform it better?
>= ;
> Thank you for you help.
>
> Bruno Andrade.
>>



-=3D This is automatically added to each message by th= e mailing script =3D-
To recover the email address of the author of the = message, please change
the strange characters on the top line to the *o* s= ign. You can also
E-mail to subscribers: CHEMISTRY*o*ccl.net or use:
   = ;   http://www.ccl.net/cgi-bin/ccl/send_ccl_message

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=0A=0A=0A
Abra sua conta no Yahoo! Mail, o =C3=BAnico sem limite de espa=C3=A7o para armazename= nto! =0A --0-1147755742-1202148099=:17881-- From owner-chemistry@ccl.net Wed Feb 6 12:37:00 2008 From: "Bruno Andrade bandradefsa ~ yahoo.com.br" To: CCL Subject: CCL: Res: CCL: Draft paper submission deadline is extended: BCBGC-08 Message-Id: <-36238-080206115735-31832-uIdCwhjue3SaaKUi8ai+qw a server.ccl.net> X-Original-From: Bruno Andrade Content-Type: multipart/alternative; boundary="0-1389506056-1202317041=:51668" Date: Wed, 6 Feb 2008 08:57:21 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Bruno Andrade [bandradefsa .. yahoo.com.br] --0-1389506056-1202317041=:51668 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Dear John Edward,=0A=0AI,m PhD. student from UEFS, Bahia - Brazil, and I`d = like to know if this meeting will provide some finnancial help to students,= such as travel expenses or hotel. As students, we don`t have too much fina= ncial resources to use in international meetings.=0A=0ASincerely,=0ABruno S= . Andrade =0APPGBIOTEC - Programa de P=C3=B3s-gradua=C3=A7=C3=A3o em Biotec= nologia - UEFS/FIOCRUZ=0AGen=C3=B4mica e Prote=C3=B4mica de microrganismos = / Modelagem Molecular=0ATels: (75)81075337 / (75)32248296=0AE-mails: bandra= defsa[*]yahoo.com.br / bandradefsa[*]gmail.com / b.andrade[*]uefs.br=0A =0APPGBIO= TEC - Graduate Program in Biotechnology=0AGenomics and Proteomics of Microo= rganisms / Molecular Modeling=0APhones: +55(75)81075337 / 32248132=0AFax: += 55(75)32248132=0AEmails: bandradefsa[*]yahoo.com.br / bandradefsa[*]gmail.com /= b.andrade[*]uefs.br=0A=0A----- Mensagem original ----=0ADe: John Edward jeed= ward=3D=3D=3Dyahoo.com =0APara: "Andrade, Bruno Si= lva " =0AEnviadas: Quarta-feira, 6 de Fev= ereiro de 2008 12:22:58=0AAssunto: CCL: Draft paper submission deadline is = extended: BCBGC-08=0A=0ADear Professors, Colleagues and Friends Kindly shar= e the announcement below with those who may be interested: thank you in adv= ance. Sincerely John Edward=0A =0A =0A BCBGC-08 Draft paper submiss= ion deadline is extended.=0A =0A The 2008 International Conference on Bi= oinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-0= 8) (website: www.PromoteResearch.org ) will be held during July 7-10 2008 i= n Orlando , FL , USA . The draft paper submission deadline is extended unt= il February 19 2008 due to several requests from the authors. The conferenc= e will be held at the same time and location where several major events (se= e below) will be taking place. =0A =0A BCBGC brings together both academ= ic and industrial scientists and developers=0A from a diverse range of disc= iplines including bioinformatics, computer science, computational biology, = genomics, proteomics and chemoinformatics. One of the main goals of the con= ference is to promote the dissemination of research to a multidisciplinary = audience and to facilitate communication among researchers in different fie= lds. Papers that demonstrate applications of existing techniques or develop= ments of new methods are equally welcomed to the conference. =0A =0A Sin= cerely=0A John Edward=0A =0A =C2=B7 International Conference on = Artificial Intelligence and Pattern Recognition (AIPR-08) =0A =C2=B7 = International Conference on Automation, Robotics and Control Systems (ARC= S-08)=0A =C2=B7 International Conference on Bioinformatics, Computa= tional Biology, Genomics and Chemoinformatics (BCBGC-08)=0A =C2=B7 = International Conference on Enterprise Information Systems and Web Technolo= gies (EISWT-08)=0A =C2=B7 International Conference on High Performa= nce Computing, Networking and Communication Systems (HPCNCS-08)=0A =C2=B7 = International Conference on Software Engineering Theory and Practice= (SETP-08) =0A =C2=B7 International Conference on Theoretical and = Mathematical Foundations of Computer Science (TMFCS-08)=0A =0A =0ABe a= better friend, newshound, and =0Aknow-it-all with Yahoo! Mobile. Try it n= ow.=0A=0A=0A=0A=0A=0A=0A Abra sua conta no Yahoo! Mail, o =C3=BAnico s= em limite de espa=C3=A7o para armazenamento!=0Ahttp://br.mail.yahoo.com/ --0-1389506056-1202317041=:51668 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
Dear John Edward,

I,m PhD. student from UEFS, Bahia - Brazil, and= I`d like to know if this meeting will provide some finnancial help to stud= ents, such as travel expenses or hotel. As students, we don`t have too much= financial resources to use in international meetings.

Sincerely,Bruno S. Andrade
 
PPGBIOTEC - Programa de P=C3=B3s-gra= dua=C3=A7=C3=A3o em Biotecnologia - UEFS/FIOCRUZ
Gen=C3=B4mica e Prote= =C3=B4mica de microrganismos / Modelagem Molecular
Tels: (75)81075337 / = (75)32248296
E-mails: bandradefsa[*]yahoo.com.br / bandradefsa[*]gmail.com /= b.andrade[*]uefs.br
 
PPGBIOTEC - Graduate Program = in Biotechnology
Genomics and Proteomics of Microorganisms / Molecular M= odeling
Phones: +55(75)81075337 / 32248132
Fax: +55(75)32248132
Em= ails: bandradefsa[*]yahoo.com.br / bandradefsa[*]gmail.com / b.andrade[*]uefs.br


=
----- Mensagem original ----
De: John Edward jeedward=3D=3D=3Dya= hoo.com <owner-chemistry[*]ccl.net>
Para: "Andrade, Bruno Silva -id#= 4bu-" <bandradefsa[*]yahoo.com.br>
Enviadas: Quarta-feira, 6 de Feve= reiro de 2008 12:22:58
Assunto: CCL: Draft paper submission deadline is = extended: BCBGC-08

Dear Professors, Colleagues and Frie=
nds
 
Kindly share the announcement below with those who may be interes= ted: thank you in advance.  
 
Sincerely<=
/tt>
John Edward
 <= /font>
 
BCBGC-08 D= raft paper submission deadline is extended.
&n= bsp;
The 2008 International Conference on Bioinformatics, Computational Biology, Genomic= s and Chemoinformatics (BCBGC-08) (website: www.PromoteResearch.org ) will be held during July 7-10 2008 in Orlando , F= L , USA .  The draft paper submission deadline= is extended until February 19 2008 due to several requests from the author= s. The conference will be held at the same time and location where several = major events (see below) will be taking place.
 
BCBGC brings together both academic a= nd industrial scientists and developers=0A from a diverse range of discipli= nes including bioinformatics, computer science, computational biology, geno= mics, proteomics and chemoinformatics. One of the main goals of the confere= nce is to promote the dissemination of research to a multidisciplinary audi= ence and to facilitate communication among researchers in different fields.= Papers that demonstrate applications of existing techniques or development= s of new methods are equally welcomed to the conference.
 
Sincerely
John Edward
 
<= div style=3D"margin-left: 31.5pt;">=C2=B7        International Conf= erence on Artificial Intelligence and Pattern Recognition (AIPR-08) =
=C2=B7        International Conferen= ce on Automation, Robotics and Control Systems (ARCS-08)
=C2=B7  = ;      International Conference on Bioinformatics, Computation= al Biology, Genomics and Chemoinformatics (BCBGC-08)
=C2=B7        International Conference on Enterprise= Information Systems and Web Technologies (EISWT-08)
= =C2= =B7   &nb= sp;    International Conference on High Performance Computing, Networkin= g and Communication Systems (HPCNCS-08)
=C2=B7 &= nbsp;      International Conference on Softw= are Engineering Theory and Practice (SETP-08)  = ;
=C2=B7=      &= nbsp;  = International Conference on Theoretical and Mathematical Foundations of Com= puter Science (TMFCS-08)

=0A

Be a b= etter friend, newshound, and =0Aknow-it-all with Yahoo! Mobile. Try it now.


=0A=0A=0A
Abra sua cont= a no Yahoo! Mail, o =C3=BAnico sem limite de espa=C3=A7o para arm= azenamento! =0A --0-1389506056-1202317041=:51668-- From owner-chemistry@ccl.net Wed Feb 6 13:12:01 2008 From: "Jeff Woodford jwoodfor_-_eou.edu" To: CCL Subject: CCL: GAMESS: normal mode displacements Message-Id: <-36239-080206002915-2498-1e/eNgEBYWZUY6WgOvrDVQ|-|server.ccl.net> X-Original-From: "Jeff Woodford" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 5 Feb 2008 20:34:58 -0800 MIME-Version: 1.0 Sent to CCL by: "Jeff Woodford" [jwoodfor(_)eou.edu] All: I thought I had a handle on this but now I am not so sure. What I'm trying to do is to displace a normal mode by a certain amount. I've used C2v water as an example. Here are the equilibrium coordinates that I have, from a GAMESS HF/cc-pVTZ calculation: H 1.0 -0.7512062957 0.0000000000 0.5886860408 H 1.0 0.7512062957 0.0000000000 0.5886860408 O 8.0 0.0000000000 0.0000000000 0.0226279184 Here are the three vibrational modes from a Hessian calculation: 7 8 9 FREQUENCY: 1752.76 4127.15 4227.05 REDUCED MASS: 1.08304 1.04483 1.08335 IR INTENSITY: 2.13690 0.34465 1.78064 1 H X 0.40932922 -0.57320805 0.54120320 Y 0.00000000 0.00000000 0.00000000 Z 0.54018293 0.38574477 -0.40780653 2 H X -0.40932922 0.57320805 0.54120320 Y 0.00000000 0.00000000 0.00000000 Z 0.54018293 0.38574477 0.40780653 3 O X 0.00000000 0.00000000 -0.06820142 Y 0.00000000 0.00000000 0.00000000 Z -0.06807108 -0.04861086 0.00000000 To convert these mass-weighted coordinates to Cartesian displacement coordinates, do I multiply each one by the square root of the reduced mass, or do I multiply each one by the square root of the mass of the atom? (Or something else?) Both ways give the sum of squares equal to one so I am now not sure which one is correct. Thanks for your help! -Jeff From owner-chemistry@ccl.net Wed Feb 6 13:49:01 2008 From: "Van Hoorn, Willem Willem.Van.Hoorn^_^pfizer.com" To: CCL Subject: CCL: Pipeline Pilot Question Message-Id: <-36240-080206102234-3686-rFu2R4IyGHa40ZIPBNn9dw*server.ccl.net> X-Original-From: "Van Hoorn, Willem" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Wed, 6 Feb 2008 14:48:15 -0000 MIME-Version: 1.0 Sent to CCL by: "Van Hoorn, Willem" [Willem.Van.Hoorn]=[pfizer.com] 0. You molecules are assumed to have been read in and available on the datastream 1. Use "Group Data by Number" to create groups of the desired size 2. Add "Count and Index Data" component to tag each group with a unique number 3. Add subprotocol with "RunToCompletion" set to true (see Implementation tab). In this subprotocol: 4. Add "Custom Manipulator (PilotScript)" with: [#]index :=3D index 5. Add "Ungroup Data" component 6. Add sd writer with file name: mydataset_part$(index).sdf -----Original Message----- > From: owner-chemistry[#]ccl.net [mailto:owner-chemistry[#]ccl.net]=20 Sent: 05 February 2008 23:23 To: Van Hoorn, Willem Subject: CCL: Pipeline Pilot Question Sent to CCL by: "Richard L. Wood" [woodx278:-:umn.edu] Hi all, I've written a protocol in Pipeline Pilot that reads in a database in smiles=20 format, coonverts it to 3D coordinates, then adds hydrogens and minimizes the structures. After this, I have it write the structures to an SDF file. The problem is that if there are a lot of molecules in the original database, this file will be very large. I've generated one that is 34 GB. I would like to be able to do something with this file, so I was wondering how or what I can do in Pipeline Pilot so that I can write out the molecules into multiple files that have fewer molecules per file? I'd like to be able to create something that I can use over and over, as opposed to just going in and having it write out x output files by having x output statements. I'm thinking that it has to be some kind of For Next loop, but I'm not sure how to write that in Pipeline Pilot. TIA,=20 Richard Richard L. Wood, Ph. D. University of Minnesota Dept. of Medicinal Chemistry, College of Pharmacy 717 Delaware St. SE Minneapolis, MN 55414-2959 woodx278^umn.edu -=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 From owner-chemistry@ccl.net Wed Feb 6 14:22:00 2008 From: "Sebastian Krapf science],[k78.eu" To: CCL Subject: CCL:G: Understanding Gaussian 03 output of simple geometry optimization Message-Id: <-36241-080206124555-26397-K4obge8o3tcACbMWpQQCSw|-|server.ccl.net> X-Original-From: "Sebastian Krapf" Date: Wed, 6 Feb 2008 12:45:51 -0500 Sent to CCL by: "Sebastian Krapf" [science],[k78.eu] Dear CCL users, I am using Gaussian 03 as a beginner and I have got a little problem in understanding the output of a simple geometry optimization of CsOH. Can anybody tell me what the two different angles in the output tell me and what do the negative numbers in the "Definition part" mean? ---------------------------- ! Optimized Parameters ! ! (Angstroms and Degrees) ! -------------------------- -------------------------- ! Name Definition Value Derivative Info. ! -------------------------------------------------------------------------------- ! R1 R(1,2) 2.6143 -DE/DX = 0.0 ! ! R2 R(2,3) 0.978 -DE/DX = 0.0 ! ! A1 L(1,2,3,-2,-1) 177.0425 -DE/DX = 0.0 ! ! A2 L(1,2,3,-1,-2) 180.0 -DE/DX = 0.0 ! ------------------------------------------------------------------------------- Thank You for Your help. Regards Sebastian __________________________________________ Sebastian Krapf Reinhold-Schneider-Str. 24 79194 Gundelfingen Germany eMail: science (at) k78.eu From owner-chemistry@ccl.net Wed Feb 6 15:01:00 2008 From: "Jeremy Besnard j10b84%%hotmail.com" To: CCL Subject: CCL: Pipeline Pilot Question Message-Id: <-36242-080206115056-30976-uLKFsMDRELJaYPQRwkrGLA|,|server.ccl.net> X-Original-From: "Jeremy Besnard" Date: Wed, 6 Feb 2008 11:50:52 -0500 Sent to CCL by: "Jeremy Besnard" [j10b84[]hotmail.com] Hi Richard, I used Pipeline Pilot last year (internship) and I managed to do it. Now that I'm back to school, I don't have access to PP, so Ill try to remind (there could be some errors, and I apologize for it). You can use the group component to group by number (for example 5000). Then you add a counter, with ]|[counter. Then you create a subprotocol with inside: -a component to define the name of the file, you can use the ]|[counter ]|[file:="c:\blabla\file_".]|[counter."sdf"; -an ungroup component -a sdf writer, and for the destination: $(file) And for the subprotocol you enable the option : "run to completion" (true) And now you will have a new file for each 5000 molecules. Note: 1. to reduce the size of a file, you can write a gz file, Pipeline does it, for the destination you write c:\blabla\file.sdf.gz, and it works. 2. For the number of molecule to group, you can use a global variable, which you can defined at the beginning. I hope you will understand what I said. Jrmy -------------------------------------------------------------------------------- > Sent to CCL by: "Richard L. Wood" [woodx278:-:umn.edu] > Hi all, > > I've written a protocol in Pipeline Pilot that reads in a database in smiles > format, coonverts it to 3D coordinates, then adds hydrogens and minimizes the > structures. After this, I have it write the structures to an SDF file. > > The problem is that if there are a lot of molecules in the original database, this file will be very large. I've generated one that is 34 GB. I would like to be able to do something with this file, so I was wondering how or what I can do in Pipeline Pilot so that I can write out the molecules into multiple files that have fewer molecules per file? I'd like to be able to create something that I can use over and over, as opposed to just going in and having it write out x output files by having x output statements. I'm thinking that it has to be some kind of For Next loop, but I'm not sure how to write that in Pipeline Pilot. > > TIA, > > Richard > > Richard L. Wood, Ph. D. > University of Minnesota > Dept. of Medicinal Chemistry, > College of Pharmacy > 717 Delaware St. SE > Minneapolis, MN 55414-2959 > woodx278^umn.edu >