Hi Hirdesh!

We just released KnowledgeSpace 1.0 = which is=20 a freely available

dataset for fragment-based design approaches = based on a=20 number

of published = synthesis=20 protocols.

http://www.biosolveit.de/datasets/

This page also contains a link to our = academic=20 collaborators who

recently published the BRICS fragment = dataset, which=20 was built

on retro-synthetic=20 analysis of=20 commercially available compounds.

Two recent papers=20 about using these kinds of datasets are = these:

http://pubs.acs.org/doi/abs/10.1021/ci800272a=

http://dx.doi.org/10.1002/cmdc.200800178

Cheers,

-Christian

________________________________________________________________= __
Dr.=20 Christian Lemmen;=20 CEO &nbs= p; =20 clemmen,+,biosolveit.de
Phone: +49-2241-2525-0 / Fax:=20 -525 &nb= sp; =20 www.biosolveit.de
BioSolveIT GmbH - An der Ziegelei 75 - 53757 = St.Augustin -=20 Germany
Gesch=E4ftsf=FChrer Dr. Christian Lemmen Amtsgericht Siegburg = HRB=20 6261

<= BR>

Von:=20 owner-chemistry+clemmen=3D=3Dbiosolveit.de,+,ccl.net=20 [mailto:owner-chemistry+clemmen=3D=3Dbiosolveit.de,+,ccl.net] Im = Auftrag von=20 hirdesh kumar hirdeshs8.,+,.gmail.com
Gesendet: = Donnerstag, 19.=20 Februar 2009 15:28
An: Lemmen, Christian =
Betreff:=20 CCL: Fragment databse

Hi All;
I am looking for any freely available fragment=20 database. Can anyone name me the same?
------=_NextPart_000_002D_01C992BF.2A13F690-- From owner-chemistry@ccl.net Thu Feb 19 14:37:00 2009 From: "Rick Venable venabler/./nhlbi.nih.gov" To: CCL Subject: CCL: NPT better than NVT for implicit solvation model? Message-Id: <-38672-090219134453-32171-Lh9yi+piO4Sj3vi0u1VM3w,,server.ccl.net> X-Original-From: Rick Venable Content-transfer-encoding: 7bit Content-type: text/plain; charset="US-ASCII" Date: Thu, 19 Feb 2009 13:09:26 -0500 Mime-version: 1.0 Sent to CCL by: Rick Venable [venabler**nhlbi.nih.gov] With implicit solvent, I'd think that NPT might be problematic; I'd expect the box size to shrink, possibly bringing the protein into contact with image copies of itself. -- Rick Venable 5635 FL/T906 Membrane Biophysics Section NIH/NHLBI Lab. of Computational Biology Bethesda, MD 20892-9314 U.S.A. (301) 496-1905 venabler AT nhlbi*nih*gov On 2/18/09 12:03 PM, "William Huang b95203004,ntu.edu.tw" wrote: > Sent to CCL by: "William Huang" [b95203004#,#ntu.edu.tw] > Dear CCLers, > > I am an undergraduate student studying the structure of amyloid fibrils > by MD simulations. I used periodic boundary condition with implicit > solvent model to mimic an infinite long fibrils. Concerning the > following two approaches: > 1. energy minimization --> NPT (200 ps) --> NVT (2 ns) > 2. energy minimization --> NPT (2.2 ns) > it's not clear to me which one is better for my project. Being a newbie > in MD simulations, I would like to know under what circumstances NPT > would be better than NVT, and vice versa. Any comments/advices are > greatly appreciated. > > Thanks a lot, > William From owner-chemistry@ccl.net Thu Feb 19 15:12:00 2009 From: "Green Power powergreen-,-gmail.com" To: CCL Subject: CCL:G: van der Waals coefficient C6 Message-Id: <-38673-090219142910-13081-FeQQSPR+uYXItaQeoOIX6Q,server.ccl.net> X-Original-From: Green Power Content-Type: multipart/alternative; boundary=000e0cd402ac51e7fc04634a8cf7 Date: Thu, 19 Feb 2009 14:28:59 -0500 MIME-Version: 1.0 Sent to CCL by: Green Power [powergreen]-[gmail.com] --000e0cd402ac51e7fc04634a8cf7 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear All, I wonder if there is any code to calculate van der Waals coefficient C6 based the polarizability calculations with Gaussian. Thanks Tian --000e0cd402ac51e7fc04634a8cf7 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear All,
I wonder if there is any code to calculate van der Waals coefficient C6 based the polarizability calculations with Gaussian. Thanks
Tian
--000e0cd402ac51e7fc04634a8cf7-- From owner-chemistry@ccl.net Thu Feb 19 15:46:00 2009 From: "Pavel A. Petukhov pap4!A!uic.edu" To: CCL Subject: CCL: atom types Message-Id: <-38674-090219151100-13397-7/BvtmUMduWwQW4IAfxbQg%x%server.ccl.net> X-Original-From: "Pavel A. Petukhov" Content-Type: multipart/alternative; boundary=-------5914908d5914908d Date: Thu, 19 Feb 2009 13:40:53 -0600 MIME-Version: 1.0 Sent to CCL by: "Pavel A. Petukhov" [pap4.:.uic.edu] This is a multi-part message in MIME format ---------5914908d5914908d Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: quoted-printable Hi Reaz, = Our recent paper may help you with the geometry and parameters for aliphati= c and aromatic azides. Pavel A. Petukhov and Gilles Pieffet. Journal of Molecular Modeling. "Param= eterization of aromatic azido group: Application for Photoaffinity Probe in= Molecular Dynamics Studies" DOI: 10.1007/s00894-009-0488-z Pasha. = *************** Pavel A. Petukhov, PhD Associate Professor Department of Medicinal Chemistry and Pharmacognosy College of Pharmacy University of Illinois at Chicago 833 S. Wood Str. Rm 539 Chicago, IL phone: 312-996-4174 fax: 312-996-7107 web: http://medchem.pharm.uic.edu = *************** = = = > From: owner-chemistry+pap4=3D=3Duic.edu**ccl.net [mailto:owner-chemistry+pap= 4=3D=3Duic.edu**ccl.net] On Behalf Of Reaz Uddin riaasuddin^-^yahoo.com Sent: Wednesday, February 18, 2009 1:01 AM To: Petukhov, Pavel A Subject: CCL: atom types = Hi Folks, I was just wondering what should be the atom types of each Nitrogen in Azid= e group (R-N=3DN+=3DN- ) in Sybyl or any common molecular operating program= s ?? Thank you so much for your time. REAZUDDIN = Research Scholar = HEJ Research Institute of Chemistry University of Karachi Karachi, Pakistan Email: riaasuddin=3D-=3Dyahoo.com, mriazuddin=3D-=3Diccs.edu = ---------5914908d5914908d Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: quoted-printable

Hi Reaz,

Our recent paper may help you with the geometry and paramete= rs for aliphatic and aromatic azides.

Pave= l A. Petukhov and Gilles Pieffet. Journal of Molecular Modeling. “Paramete= rization of aromatic azido group: Application for Photoaffinity Probe in Molecular Dynamics Studies”
DOI: 10.1007/s00894-009-0488-z

Pasha.

***************

Pavel A. Petukhov, PhD

Associate Professor

Department of Medicinal Chemistry and Pharmacognosy

College of Pharmacy

University of Illinois at Chicago

833 S. Wood Str. Rm 539

Chicago, IL

phone: 312-996-4174

fax: 312-996-7107

web: http://medchem.pharm.uic.edu

***************

From: owner-chemistry+pap4=3D=3Duic.edu**ccl.net [mailto:owner-chemistry+pap4=3D=3Duic.edu**ccl.net] On Behalf Of Reaz= Uddin riaasuddin^-^yahoo.com
Sent: Wednesday, February 18, 2009 1:01 AM
To: Petukhov, Pavel A
Subject: CCL: atom types

Hi Folks,<= /o:p>

I was just wondering w= hat should be the atom types of each Nitrogen in Azide group (= R-N=3DN^{+=3DN^-} ) in Sybyl or any common molecular operating programs ??

Thank you so much for = your time.

REAZUDDIN
Research Scholar
HEJ Research Institute of Chemistry
University of Karachi
Karachi, Pakistan
Email: riaasuddin=3D-=3Dyahoo.com, mriazuddin=3D-=3Diccs.edu

---------5914908d5914908d-- From owner-chemistry@ccl.net Thu Feb 19 16:33:00 2009 From: "Curt M. Breneman brenec() rpi.edu" To: CCL Subject: CCL: Reminder - March 16th Closing Date for COMP Symposium submissions on OASys for Washington, D.C. Meeting! Message-Id: <-38675-090219155256-13039-NoDD88GCudcgXK0JRFA7Pg*|*server.ccl.net> X-Original-From: "Curt M. Breneman" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0823_01C9929F.903E09D0" Date: Thu, 19 Feb 2009 14:37:17 -0500 MIME-Version: 1.0 Sent to CCL by: "Curt M. Breneman" [brenec[a]rpi.edu] This is a multi-part message in MIME format. ------=_NextPart_000_0823_01C9929F.903E09D0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Reminder: $1,000 prize to be awarded for the best talk on Emerging Technologies in Computational Chemistry at the 238th ACS national meeting, Washington, D.C. (Sponsored by the ACS Division of Computers in Chemistry and Schrodinger, Inc) The Computers in Chemistry Division (COMP) of the ACS will hold the eighth annual Symposium on Emerging Technologies in Computational Chemistry at the American Chemical Society National Meeting, Washington, D.C., August 15-20, 2009. The objective of the symposium is to stimulate, reward, and publicize major methodological advances in computational chemistry. The talks will be evaluated by a Panel of Experts on the quality of the presentation and the impact that the research will have on the future of computational chemistry and allied sciences. The symposium is ideal for presenting your latest and best research on new techniques, applications and software development. Schrodinger, Inc. sponsors the $1,000 award for the best talk at the symposium. All are invited to participate. To enter the competition, please submit a regular short ACS abstract via http://oasys.acs.org/ prior to the OAsys deadline (believe it or not, OAsys opens for the Washington, D.C. meeting on January 19th, and closes on March 16th). It is also necessary to email a long (~1,000-word) abstract to the organizer. The presentations must be original, novel and concise. After receipt, the long abstracts will be evaluated by experts to determine which individuals will be selected to give oral presentations during the half-day award symposium. Finalists will be notified well in advance of the meeting. Presentations submitted through OAsys that cannot be part of the Emerging Technologies Symposium will be rescheduled in another appropriate COMP session at the Washington meeting. Inquiries and applications should sent to: Prof. Curt M. Breneman> Director, RECCR Center Department of Chemistry Rensselaer Polytechnic Institute Troy, NY 12180 E-mail: brenec_at_rpi.edu ------=_NextPart_000_0823_01C9929F.903E09D0 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Reminder:

<= /o:p>

$1,000 = prize to be awarded for the best talk on Emerging Technologies in Computational = Chemistry at the 238th ACS national meeting, Washington, D.C. =

<= /o:p>

(Sponsored = by the ACS Division of Computers in Chemistry and Schrodinger, = Inc)

The Computers in Chemistry Division (COMP) of the ACS = will hold the eighth

annual Symposium on Emerging Technologies in Computational Chemistry at = the

American Chemical Society National Meeting, = Washington, D.C., August

15-20, 2009. The objective of the symposium is = to stimulate, reward, and

publicize major methodological advances in = computational chemistry.

The talks will be evaluated by a Panel of Experts on = the quality of the

presentation and the impact that the research will = have on the future of

computational chemistry and allied sciences. The = symposium is ideal for

presenting your latest and best research on new = techniques, applications

and software development. Schrodinger, Inc. sponsors = the $1,000 award for

the best talk at the = symposium.

All are invited to participate. To enter the = competition, please submit

a regular short ACS abstract via = http://oasys.acs.org/ prior to the OAsys

deadline (believe it or not, OAsys opens for the = Washington, D.C. meeting on

January 19^th, and closes on March 16th). = It is also necessary to email a long (~1,000-word) = abstract

to the organizer. The presentations must be original, = novel and concise.

After receipt, the long abstracts will be evaluated = by experts to determine

which individuals will be selected to give oral presentations during the half-day award

symposium. Finalists will be notified well in = advance of the meeting.

Presentations submitted through OAsys that cannot be = part of the Emerging

Technologies Symposium will be rescheduled in another appropriate COMP

session at the Washington meeting.

Inquiries and applications should sent = to:

Prof. Curt M. Breneman> =

Director, RECCR Center

Department of Chemistry

Rensselaer Polytechnic = Institute

Troy, NY 12180

E-mail: = brenec_at_rpi.edu

------=_NextPart_000_0823_01C9929F.903E09D0-- From owner-chemistry@ccl.net Thu Feb 19 17:19:00 2009 From: "Green Power powergreen::gmail.com" To: CCL Subject: CCL:G: TDDFT expansion coefficients Message-Id: <-38676-090219171741-21087-cQGx0Fwwm8GSjhWGszuO0g[-]server.ccl.net> X-Original-From: Green Power Content-Type: multipart/alternative; boundary=001517573db4fd9f7504634ce652 Date: Thu, 19 Feb 2009 17:17:30 -0500 MIME-Version: 1.0 Sent to CCL by: Green Power [powergreen^^gmail.com] --001517573db4fd9f7504634ce652 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi, Could you tell me how to print the full list of coefficients in the CI expansion for TDDFT calculations using Gaussian? Thank you in advance. Tian --001517573db4fd9f7504634ce652 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi,
Could you tell me how to print the full list of coefficients in the CI expansion for TDDFT calculations using Gaussian? Thank you in advance.
Tian
--001517573db4fd9f7504634ce652-- From owner-chemistry@ccl.net Thu Feb 19 18:36:01 2009 From: "Lukasz Cwiklik cwiklik(-)gmail.com" To: CCL Subject: CCL: NPT better than NVT for implicit solvation model? Message-Id: <-38677-090219182721-8576-kecOJ/JMXe/AH/MruxudiA**server.ccl.net> X-Original-From: Lukasz Cwiklik Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 20 Feb 2009 01:27:05 +0200 MIME-Version: 1.0 Sent to CCL by: Lukasz Cwiklik [cwiklik]^[gmail.com] Dear William, To put it simple, NPT ensemble would be better if you need/suppose the volume of your simulation box to be changed during your MD run. A general example are simulations where you are starting simulations for a newly built system and it is not fully equilibrated in a given box, or if the system by its physical nature would expand/collapse during your MD. A "bio" oriented example of such a situation are MD simulations of phospholipid membranes, where you apply pressure coupling in parallel to the surface of the membrane allowing for changes of area per lipid. In your case, the answer depends on how you prepared your system for simulations and how your fibrils are oriented into the box. I suppose, your fibrils are located along one of the axis, and if you wish to allow for their stretching you need to use NPT (with pressure coupling at least in the direction of fibrils). Best, Lukasz -- Lukasz Cwiklik http://cwiklik.wordpress.com On Wed, Feb 18, 2009 at 7:03 PM, William Huang b95203004,ntu.edu.tw wrote: > > Sent to CCL by: "William Huang" [b95203004#,#ntu.edu.tw] > Dear CCLers, > > I am an undergraduate student studying the structure of amyloid fibrils > by MD simulations. I used periodic boundary condition with implicit > solvent model to mimic an infinite long fibrils. Concerning the > following two approaches: > 1. energy minimization --> NPT (200 ps) --> NVT (2 ns) > 2. energy minimization --> NPT (2.2 ns) > it's not clear to me which one is better for my project. Being a newbie > in MD simulations, I would like to know under what circumstances NPT > would be better than NVT, and vice versa. Any comments/advices are > greatly appreciated. > > Thanks a lot, > William> > > From owner-chemistry@ccl.net Thu Feb 19 19:11:00 2009 From: "Lukasz Cwiklik cwiklik_+_gmail.com" To: CCL Subject: CCL: Gromacs installation on Dell Ubuntu Message-Id: <-38678-090219183500-9193-xjzmDL7/S1jO0TH0++ZsCA]-[server.ccl.net> X-Original-From: Lukasz Cwiklik Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 20 Feb 2009 01:34:46 +0200 MIME-Version: 1.0 Sent to CCL by: Lukasz Cwiklik [cwiklik#,#gmail.com] Dear Maura, Have you seen this "Quick and dirty installation" guide? http://wiki.gromacs.org/index.php/quick_and_dirty_installation It gives a concise yet full description of the installation process. Best, Lukasz -- Lukasz Cwiklik http://cwiklik.wordpress.com On Tue, Feb 17, 2009 at 6:35 PM, Maura Mooney mmooney05()qub.ac.uk wrote: [...] > I am having problem configuring gromacs on my dell machine. I have unzipped the gromacs archive and also the fftw3...tar.gz file (required as a prerequisite). The next step requires > > cd to the gromacs directory and ./configure. > > But I can't seem to locate the gromacs directory, or the configure program, thus I cannot go any further with the configuration/installation. From owner-chemistry@ccl.net Thu Feb 19 19:47:01 2009 From: "Anders Blom anders.blom*o*quantumwise.com" To: CCL Subject: CCL: k point mesh Message-Id: <-38679-090219182248-8151-eTV4VU/pEWHPZfJVxI97+A,,server.ccl.net> X-Original-From: Anders Blom Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 19 Feb 2009 23:20:02 +0100 MIME-Version: 1.0 Sent to CCL by: Anders Blom [anders.blom^^^quantumwise.com] Hello David, the literature you refer to is most likely calculations performed using TranSIESTA (Brandbyge et al., Phys. Rev. B 65, 165401 (2002)) or a similar code that uses the same methodology (e.g. Atomistix ToolKit or Smeagol, although I am not familiar with the deeper details of the latter software). The key point of this method is that the boundary conditions are actually not periodic in the z direction. Instead, open boundary conditions are used, in order to apply a voltage across the structure, so that one can compute the electron current under finite bias. The system (a so-called two-probe) is subdivided into three parts, left and right electrodes, which are bulk-like (semi-infinite), and a central scattering region over which the bias is actually applied, and where the non-equilibrium electron distribution can be computed using Green's function techniques. To understand why one needs many Kz-points in this case, assume that you have an ideal system, i.e. the electrodes are identical to the central region. Let HL, HC, HR be the Hamiltonian of the left electrode, central region, and right electrode, respectively. HL, HR are calculated under periodic boundary conditions, while HC is evaluated (self-consistently) calculated with open boundary conditions using self-energies obtained from HL and HR. Now, clearly you will only get integer transmission in this system if HL=HR=HC. To obtain this, the same k-point sampling should be used in the Kx and Ky directions for the electrode and subsequent two-probe calculation (with open boundary conditions). This point is quite trivial. In the z-direction, however, the two-probe calculation corresponds to an infinite number of Kz points, thus you need a lot of k-points in the z-direction for the electrode calculation to ensure the same level of accuracy. Generally, the literature values for Kz may be a little conservative, but it is relatively inexpensive since these k-points are only required for the electrode calculation which is the smaller and faster part of the whole computation. In case you have specific questions about or general interest in Atomistix ToolKit, you can also post questions on its official user forum, http://quantumwise.com/forum. Anders Blom -- Anders Blom, Ph.D. QuantumWise A/S http://www.quantumwise.com David Cornil cornildavid^yahoo.fr wrote: > Sent to CCL by: "David Cornil" [cornildavid()yahoo.fr] > Dear CCL'users > > I have a question about the number of k point we need to perform a calculation in periodic boundary conditions of specific systems like [metalic electrode]-[molecule]-[metalic electrode] with molecule along the z axis. Some litteratures mention k point parameters around 1x1x100 or 3x3x100 for Brillouin zone integration. It surprising me because in interface system like SAM in periodic condition k point parameters are like 8x8x1. Can you explain to me the reasons of this difference ? > > Thank you in advance > > David A. M. Cornil > Ph.D Student > University of Mons-Hainaut > Belgium > > >