From owner-chemistry@ccl.net Sun Apr 19 06:14:00 2009 From: "Lukasz Cwiklik cwiklik#,#gmail.com" To: CCL Subject: CCL: Forcefield parameters transformation - derivation ? Message-Id: <-39114-090419060559-31471-53+o1hVeJM2XQqPXhbeUug-,-server.ccl.net> X-Original-From: Lukasz Cwiklik Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-2 Date: Sun, 19 Apr 2009 13:05:44 +0300 MIME-Version: 1.0 Sent to CCL by: Lukasz Cwiklik [cwiklik(a)gmail.com] Dear Marek, Take a look at Antechamber which is a part of Amber package: http://ambermd.org/antechamber/antechamber.html Particularly, look at "Tutorials and Examples". Antchamber can assist in a derivation of force field parameters for new atom types and residues. It generally works according to your (B) strategy (i.e., some info is taken from quantum calculations albeit some parameters, if available, are taken from a standard Generalized Amber Force Field). Best, Lukasz --=20 Lukasz Cwiklik http://cwiklik.wordpress.com On Mon, Apr 6, 2009 at 6:37 PM, Marek Mal=FD marek.maly-x-ujep.cz wrote: > > Sent to CCL by: =3D?iso-8859-2?Q?Marek_Mal=3DFD?=3D [marek.maly=3D=3D=3Du= jep.cz] > Dear all, > > I would like to simulate carbosilanes and later their complexes with > organic macromolecules using Amber software. > > Unfortunately Amber forcefields do not contain proper ff parameters for > silicon. > > In spite of this fact there is still possibility to simulate my Si-based > molecules in Amber > but I have to find proper parameters (e.g. bond, angle, dihedral) somewhe= re > elsewhere ... > > I need ff parameters for Si in this contexts: > > C-C-C-Si, Si-O-C-C, C-Si-C-H etc. > > > So I see here two solutions: > > > A) > > To import relevant parameters from another forcefields like CVFF, PCFF, M= M2, > MM3 ... > > Regarding to this point it would be nice to have some routine which could= be > able to convert > one forcefield file XYZ to ff file written in Amber format. If possible n= ot > to > transform just text formating of the source XYZ ff file with respect of > Amber formating, > but also to transform properly the parameters values with respect to > eventual diferences in units or analytic > formulas for interatomic forces. > > > B) > > To derive all the necessary parameters using some intelligent (probably > quantum mechanics based) software which could be able > to do this analysis for small residua provided for example in PDB format. > Again would be nice to have this parameters > in format compatible with Amber ff. > > I am kindly asking for any (even only partial) information regarding to t= his > topic or just for redirecting to > relevant information resources. Of course that I will be grateful not onl= y > for info related to some appropriate SW > which can help me regarding to A) or B) but I will also appreciate any in= fo > based on own experiences, strategies, suggestions, warnings =A0... > regarding to this topic. > > Best regards, > > =A0 Marek > > > > -- > Tato zpr=E1va byla vytvo=F8ena p=F8evratn=FDm po=B9tovn=EDm klientem Oper= y: > http://www.opera.com/mail/ > > > > -=3D This is automatically added to each message by the mailing script = =3D-> =A0 =A0> =A0 =A0=A0 =A0 http://www.ccl.net/chemistry/sub_unsub.sht= ml> > Job: http://www.ccl.net/jobsConferences: > http://server.ccl.net/chemistry/announcements/conferences/> =A0 =A0> > > From owner-chemistry@ccl.net Sun Apr 19 13:38:01 2009 From: "hirdesh kumar hirdeshs8],[gmail.com" To: CCL Subject: CCL: Distance Constraints in Discovery studio "Catalyst" Message-Id: <-39115-090419133054-19259-JlIneMCaW8AOmX7tfEcuhw[*]server.ccl.net> X-Original-From: hirdesh kumar Content-Type: multipart/alternative; boundary=001485f880e4c92c590467eaecb9 Date: Sun, 19 Apr 2009 21:59:59 +0530 MIME-Version: 1.0 Sent to CCL by: hirdesh kumar [hirdeshs8+/-gmail.com] --001485f880e4c92c590467eaecb9 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi all; I am using catalyst4.1 "HIPHOP" module of discovery studio. I am unable to explore the "distance measurement" between different pharmacophoric features. Is there anyone familiar with the same. --001485f880e4c92c590467eaecb9 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi all;
I am using catalyst4.1 "HIPHOP" module of discovery studio. I am unable to explore the "distance measurement" between different pharmacophoric features. Is there anyone familiar with the same. --001485f880e4c92c590467eaecb9-- From owner-chemistry@ccl.net Sun Apr 19 14:12:01 2009 From: "John Edward jeedward,+,yahoo.com" To: CCL Subject: CCL: Extended draft paper submission: BCBGC-09 call for papers Message-Id: <-39116-090419130011-15879-1TX1ljP7QbCSnUe4f9MR0w**server.ccl.net> X-Original-From: John Edward Content-Type: multipart/alternative; boundary="0-2009169913-1240156730=:93521" Date: Sun, 19 Apr 2009 08:58:50 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: John Edward [jeedward!=!yahoo.com] --0-2009169913-1240156730=:93521 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Extended draft paper submission: BCBGC-09 call for papers =A0 This Extended Call for Papers for the 2009 International Conference on Bioi= nformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-09)= (website: http://www.PromoteResearch.org ) is for those who didn't get a c= hance to submit the papers for the earlier call for papers. The papers rece= ived and accepted in response to this extended call for papers will be incl= uded in the final version of the respective conference proceedings. These p= roceedings will be either ready by the time of the conference (i.e., they w= ill be available during the conference) or soon after the conference (befor= e the end of August 2009), based how fast the proceedings can be prepared.= =20 Note: If you have already submitted a paper (whether accepted or rejected o= r currently under review) for MULTICONF-09, please DO NOT submit that paper= again to this extended call for papers.=20 IMPORTANT DATES:=20 Draft paper submission date: May 11, 2009=20 Acceptance/rejection decision: May 21, 2009 Camera ready paper and copyright and pre-registration due: May 28, 2009 Conference dates: July 13-16, 2009 =A0 =A0 BCBGC-09 will be held during July 13-16 2009 in Orlando, FL, USA. The confe= rence will take place at the same time and venue where several other intern= ational conferences are taking place. The other conferences include: =B7=A0=A0=A0=A0=A0=A0=A0=A0 International Conference on Artificial Intellig= ence and Pattern Recognition (AIPR-09)=20 =B7=A0=A0=A0=A0=A0=A0=A0=A0 International Conference on Automation, Robotic= s and Control Systems (ARCS-09) =B7=A0=A0=A0=A0=A0=A0=A0=A0 International Conference on Enterprise Informat= ion Systems and Web Technologies (EISWT-09) =B7=A0=A0=A0=A0=A0=A0=A0=A0 International Conference on High Performance Co= mputing, Networking and Communication Systems (HPCNCS-09)=20 =B7=A0=A0=A0=A0=A0=A0=A0=A0 International Conference on Information Securit= y and Privacy (ISP-09) =B7=A0=A0=A0=A0=A0=A0=A0=A0 International Conference on Recent Advances in = Information Technology and Applications (RAITA-09) =B7=A0=A0=A0=A0=A0=A0=A0=A0 International Conference on Software Engineerin= g Theory and Practice (SETP-09)=20 =B7=A0=A0=A0=A0=A0=A0=A0=A0 International Conference on Theory and Applicat= ions of Computational Science (TACS-09) =B7=A0=A0=A0=A0=A0=A0=A0=A0 International Conference on Theoretical and Mat= hematical Foundations of Computer Science (TMFCS-09) =A0 The website http://www.PromoteResearch.org contains more details. =A0 Sincerely John Edward Publicity committee=0A=0A=0A --0-2009169913-1240156730=:93521 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable

Extended draft paper submission: BCBGC= -09 call for papers

 

This Extended Call for Papers for the 2009 International Conference on Bioinformatics, Computational Biology, Ge= nomics and Chemoinformatics (BCBGC-09) (website: http://www.PromoteResearch.org= ) is for those who didn't get a chance to = submit the papers for the earlier call for papers. The papers received and = accepted in response to this extended call for papers will be included in the final version of the resp= ective conference proceedings. These proceedings will be either ready by th= e time of the conference (i.e., they will be available during the conferenc= e) or soon after the conference (before the end of August 2009), based how = fast the proceedings can be prepared.

Note: If you have already submitted = a paper (whether accepted or rejected or currently under review) for MULTIC= ONF-09, please DO NOT submit that paper again to this extended call for pap= ers.


IMPORTANT DATES:

Draft paper submission date: May 11, 2009
Acceptance/re= jection decision: May 21, 2009
Camera ready paper and copyright and pre-= registration due: May 28, 2009
Conference dates: July 13-16, 2009=

 

 

BCBGC-09 will be held during J= uly 13-16 2009 in Orlando, FL, USA. The conference will take place at the s= ame time and venue where several other international conferences are taking= place. The other conferences include:

=B7         <= /FONT>

=B7         =B7         =B7         =B7         =B7         =B7         =B7         =B7          

The website h= ttp://www.PromoteResearch.org contains more details.

 

Sincerely

John Edward

Publicity committee


=0A= =0A=0A=0A --0-2009169913-1240156730=:93521--