From owner-chemistry@ccl.net Tue Nov 17 00:44:01 2015 From: "Yingbin Ge yingbin.ge%x%gmail.com" To: CCL Subject: CCL:G: How to run a B3LYP-D3 calculation in GAMESS program? Message-Id: <-51880-151117004146-6861-tbS7X+q/weVnPs6lFdytJg * server.ccl.net> X-Original-From: Yingbin Ge Content-Type: multipart/alternative; boundary=001a114a847ce834da0524b5fa3c Date: Mon, 16 Nov 2015 21:41:40 -0800 MIME-Version: 1.0 Sent to CCL by: Yingbin Ge [yingbin.ge,gmail.com] --001a114a847ce834da0524b5fa3c Content-Type: text/plain; charset=UTF-8 Maryam, If you search for Grimme in the INPUT.DOC file, you will get sth. like the following: empirical dispersion corrections: DC = a flag to turn on Grimme's empirical dispersion correction, involving scaled R**(-6) terms. Parameters are basis set and functional dependent, so they exist for only a few DFTTYP. See R.Peverati and K.K.Baldridge J.Chem.Theory Comput. 4, 2030(2008) for more values, which can be entered using DCPAR. (default=.FALSE., except when DFTTYP=B97-D) N.B. This empiricism may also be added to plain Hartree-Fock, by choosing DFTTYP=NONE with DC=.T. DCOLD = a flag to use Grimme's original 2004 dispersion correction, this forces DC=.T. (default=.FALSE.) DCPAR = Grimme's parameter S6 for scaling a C6 term added as an empirical correction to otherwise unchanged functionals (showing Grimme's default for S6): BLYP(1.20), PBE(0.75), BP86(1.05), TPSS(1.00), B3LYP(1.05), B2PLYP(0.55). For B97-D, the -D also changes the original functional, and the scale factor is 1.25. DC works for other functionals, if you make up your own value for DCPAR. DCEXP = Grimme's parameter SR to scale the van der Waals radii in the damping function. Relevant if DC=.T. (default=1.0, except B2PLYP which uses 1.30) Yingbin Ge On Mon, Nov 16, 2015 at 7:52 AM, Maryam Sangani maryamrahmani794 . yahoo.com wrote: > > Sent to CCL by: "Maryam Sangani" [maryamrahmani794(0)yahoo.com] > I want to do calculations using dispersion corrected B3LYP level in > GAMESS program. I know how to run it in Gaussian 09 with the keyword > iop(3/124=3). How to run a B3LYP-D3 calculation in GAMESS? > It will be great if you can clarify me about these points. > Thank you for the help, > Regards > Maryam> > > --001a114a847ce834da0524b5fa3c Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Maryam,

If you search for Grim= me in the INPUT.DOC file, you will get sth. like the following:

=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= empirical dispersion corrections:

DC=C2=A0=C2=A0=C2=A0=C2=A0 =3D a = flag to turn on Grimme's empirical dispersion
=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0 correction, involving scaled R**(-6) terms.
= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 Parameters are basis set a= nd functional
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 dependent= , so they exist for only a few DFTTYP.
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0 See R.Peverati and K.K.Baldridge J.Chem.Theory
=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 Comput. 4, 2030(2008) for more valu= es, which can
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 be entere= d using DCPAR.
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 (default= =3D.FALSE., except when DFTTYP=3DB97-D)
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0 N.B.=C2=A0 This empiricism may also be added to plain=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 Hartree-Fock, by choosing= DFTTYP=3DNONE with DC=3D.T.

DCOLD=C2=A0 =3D a flag to use Grimme= 9;s original 2004 dispersion
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0 correction, this forces DC=3D.T. (default=3D.FALSE.)

DCPAR=C2= =A0 =3D Grimme's parameter S6 for scaling a C6 term added
=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 as an empirical correction to other= wise unchanged
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 function= als (showing Grimme's default for S6):
=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0 BLYP(1.20), PBE(0.75), BP86(1.05), TPSS(1.00),
=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 B3LYP(1.05), B2PLYP(0.55).=C2= =A0 For B97-D, the -D also
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0 changes the original functional, and the scale
=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0 factor is 1.25.=C2=A0 DC works for other functi= onals,
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 if you make up y= our own value for DCPAR.

DCEXP=C2=A0 =3D Grimme's parameter SR t= o scale the van der Waals
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0 radii in the damping function.=C2=A0 Relevant if DC=3D.T.
=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 (default=3D1.0, except B2PLYP which= uses 1.30)

Yingbin Ge

<= div class=3D"gmail_extra">
On Mon, Nov 16, 20= 15 at 7:52 AM, Maryam Sangani maryamrahmani794 . yahoo.com <owner-chemistry(~)ccl.net> wrote:
<= blockquote class=3D"gmail_quote" style=3D"margin:0px 0px 0px 0.8ex;border-l= eft:1px solid rgb(204,204,204);padding-left:1ex">
Sent to CCL by: "Maryam=C2=A0 Sangani" [maryamrahmani794(0)yahoo.com]<= br> =C2=A0I want to do calculations using dispersion corrected B3LYP level in G= AMESS program. I know how to run it in Gaussian 09 with the keyword iop(3/1= 24=3D3).=C2=A0 How to run a B3LYP-D3 calculation in GAMESS?
It will be great if you can clarify me about these points.
Thank you for the help,
Regards
Maryam



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--001a114a847ce834da0524b5fa3c-- From owner-chemistry@ccl.net Tue Nov 17 06:46:01 2015 From: "katy emily kellett k.kellett]_[herts.ac.uk" To: CCL Subject: CCL: Clustering molecular conformations Message-Id: <-51881-151117064227-20129-BDDhWlMwPqZH5LkqbGhcTw::server.ccl.net> X-Original-From: "katy emily kellett" Date: Tue, 17 Nov 2015 06:42:26 -0500 Sent to CCL by: "katy emily kellett" [k.kellett+/-herts.ac.uk] Hi, I was wondering if anyone knows of a software or program that can cluster small molecule conformations from trajectories. I have found a number that will do it with peptides, but they are not suitable for small molecules, that I can tell. Would appreciate any advice on the topic. Thanks very much in advance, Katy From owner-chemistry@ccl.net Tue Nov 17 08:34:00 2015 From: "Shahar Keinan skeinan%a%gmail.com" To: CCL Subject: CCL: Clustering molecular conformations Message-Id: <-51882-151117083306-7832-jaEmQoKaxaNeptGDzKHjhA__server.ccl.net> X-Original-From: Shahar Keinan Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Tue, 17 Nov 2015 08:32:55 -0500 MIME-Version: 1.0 Sent to CCL by: Shahar Keinan [skeinan.:.gmail.com] DIVCF from Michel Petitjean can do this: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#DIVCF The problem is that you can't control the number/size of clusters. Best, Shahar On 11/17/15 6:42 AM, katy emily kellett k.kellett]_[herts.ac.uk wrote: > Sent to CCL by: "katy emily kellett" [k.kellett+/-herts.ac.uk] > Hi, > > I was wondering if anyone knows of a software or program that can cluster > small molecule conformations from trajectories. I have found a number that > will do it with peptides, but they are not suitable for small molecules, > that I can tell. > > Would appreciate any advice on the topic. > > Thanks very much in advance, > > Katy> > -- ------------------------------------------------------ Shahar Keinan (919) 357 5319 From owner-chemistry@ccl.net Tue Nov 17 09:09:00 2015 From: "Christoph Bannwarth cbannwar..uni-bonn.de" To: CCL Subject: CCL: How to run a B3LYP-D3 calculation in GAMESS program? Message-Id: <-51883-151117035959-2174-1HJhHEg5BK0lwtcZBy+Y+Q[*]server.ccl.net> X-Original-From: Christoph Bannwarth Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=utf-8; format=flowed Date: Tue, 17 Nov 2015 09:59:01 +0100 MIME-Version: 1.0 Sent to CCL by: Christoph Bannwarth [cbannwar!^!uni-bonn.de] Dear Maryam, according to the GAMESS input documentation, the D3 correction will be chosen by default for most functionals when specifying DC in your input. To be sure, you should set in the DFT block. IDCVER = 3 Another note: It seems in GAMESS only the so called zero-damped version of D3 is implemented. In 2011, there has been a revision of the damping function in D3: http://onlinelibrary.wiley.com/doi/10.1002/jcc.21759/abstract This variant is called the Becke-Johnson damped version of D3. It is more physically sound and should be preferred over the zero-damped variant. Typically, it is abbreviated by D3BJ, D3(BJ) or just D3, as it became the default scheme in recent years. To use it, you can download the standalone D3 code from Grimme's website: http://www.thch.uni-bonn.de/tc/index.php?section=downloads&subsection=DFT-D3&lang=english Furthermore, it is implemented in the quantum chemistry package ORCA which is free of charge: https://orcaforum.cec.mpg.de/ The latter option might be more convenient to you, if you want to run geometry optimizations with B3LYP-D3BJ. Best regards, Christoph On 11/17/15 06:41, Yingbin Ge yingbin.ge%x%gmail.com wrote: > Maryam, > > If you search for Grimme in the INPUT.DOC file, you will get sth. like > the following: > > empirical dispersion corrections: > > DC = a flag to turn on Grimme's empirical dispersion > correction, involving scaled R**(-6) terms. > Parameters are basis set and functional > dependent, so they exist for only a few DFTTYP. > See R.Peverati and K.K.Baldridge J.Chem.Theory > Comput. 4, 2030(2008) for more values, which can > be entered using DCPAR. > (default=.FALSE., except when DFTTYP=B97-D) > N.B. This empiricism may also be added to plain > Hartree-Fock, by choosing DFTTYP=NONE with DC=.T. > > DCOLD = a flag to use Grimme's original 2004 dispersion > correction, this forces DC=.T. (default=.FALSE.) > > DCPAR = Grimme's parameter S6 for scaling a C6 term added > as an empirical correction to otherwise unchanged > functionals (showing Grimme's default for S6): > BLYP(1.20), PBE(0.75), BP86(1.05), TPSS(1.00), > B3LYP(1.05), B2PLYP(0.55). For B97-D, the -D also > changes the original functional, and the scale > factor is 1.25. DC works for other functionals, > if you make up your own value for DCPAR. > > DCEXP = Grimme's parameter SR to scale the van der Waals > radii in the damping function. Relevant if DC=.T. > (default=1.0, except B2PLYP which uses 1.30) > > Yingbin Ge From owner-chemistry@ccl.net Tue Nov 17 09:44:01 2015 From: "Andreas Klamt klamt###cosmologic.de" To: CCL Subject: CCL: Clustering molecular conformations Message-Id: <-51884-151117091153-24044-4Rv8/p1PN7vBl3MeU3w+/A[*]server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-15 Date: Tue, 17 Nov 2015 15:11:42 +0100 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt~!~cosmologic.de] Hi back, our COSMOconf software does generate and cluster conformations of small molecules with respect to geometry, energy, and with respect to their importance (chemical potential) in different solvents. It can also be fed with external conformational sets, e.g. from your trajectories. Best regards Andreas Am 17.11.2015 um 12:42 schrieb katy emily kellett k.kellett]_[herts.ac.uk: > Sent to CCL by: "katy emily kellett" [k.kellett+/-herts.ac.uk] > Hi, > > I was wondering if anyone knows of a software or program that can cluster > small molecule conformations from trajectories. I have found a number that > will do it with peptides, but they are not suitable for small molecules, > that I can tell. > > Would appreciate any advice on the topic. > > Thanks very much in advance, > > Katy> > > -- -------------------------------------------------- Prof. Dr. Andreas Klamt CEO / Geschäftsführer COSMOlogic GmbH & Co. KG Imbacher Weg 46 D-51379 Leverkusen, Germany phone +49-2171-731681 fax +49-2171-731689 e-mail klamt!=!cosmologic.de web www.cosmologic.de [University address: Inst. of Physical and Theoretical Chemistry, University of Regensburg] HRA 20653 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt Komplementaer: COSMOlogic Verwaltungs GmbH HRB 49501 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt From owner-chemistry@ccl.net Tue Nov 17 10:19:01 2015 From: "Rajarshi Guha rajarshi.guha * gmail.com" To: CCL Subject: CCL: Clustering molecular conformations Message-Id: <-51885-151117095938-28679-MIH3XV5k1dQVYJW7m25A7w-.-server.ccl.net> X-Original-From: Rajarshi Guha Content-Type: multipart/alternative; boundary=94eb2c07fb1ab75ce70524bdc5c5 Date: Tue, 17 Nov 2015 09:59:28 -0500 MIME-Version: 1.0 Sent to CCL by: Rajarshi Guha [rajarshi.guha{=}gmail.com] --94eb2c07fb1ab75ce70524bdc5c5 Content-Type: text/plain; charset=UTF-8 If you're an R user you could look at bio3d ( https://cran.fhcrc.org/web/packages/bio3d/index.html) though it does seem to be protein centric On Tue, Nov 17, 2015 at 6:42 AM, katy emily kellett k.kellett]_[herts.ac.uk wrote: > > Sent to CCL by: "katy emily kellett" [k.kellett+/-herts.ac.uk] > Hi, > > I was wondering if anyone knows of a software or program that can cluster > small molecule conformations from trajectories. I have found a number that > will do it with peptides, but they are not suitable for small molecules, > that I can tell. > > Would appreciate any advice on the topic. > > Thanks very much in advance, > > Katy> > > -- Rajarshi Guha | http://blog.rguha.net NIH Center for Advancing Translational Science --94eb2c07fb1ab75ce70524bdc5c5 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
If you're an R user you could look at bio3d (https://cran.fhcr= c.org/web/packages/bio3d/index.html) though it does seem to be protein = centric

On T= ue, Nov 17, 2015 at 6:42 AM, katy emily kellett k.kellett]_[herts.ac.uk <owner-chemistry|ccl.net> wrote:

Sent to CCL by: "katy emily kellett" [k.kellett+/-herts.ac.uk]
Hi,

I was wondering if anyone knows of a software or program that can cluster small molecule conformations from trajectories. I have found a number that<= br> will do it with peptides, but they are not suitable for small molecules, that I can tell.

Would appreciate any advice on the topic.

Thanks very much in advance,

Katy



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NIH Center for Advancing Transla= tional Science
--94eb2c07fb1ab75ce70524bdc5c5-- From owner-chemistry@ccl.net Tue Nov 17 12:13:01 2015 From: "Daniel Roe daniel.r.roe-.-gmail.com" To: CCL Subject: CCL: Clustering molecular conformations Message-Id: <-51886-151117120944-28196-ggSUbLwqKNnxTUQE7yTpPQ|server.ccl.net> X-Original-From: Daniel Roe Content-Type: text/plain; charset=UTF-8 Date: Tue, 17 Nov 2015 10:09:38 -0700 MIME-Version: 1.0 Sent to CCL by: Daniel Roe [daniel.r.roe=gmail.com] Hi, You could try using CPPTRAJ, which is freely available as part of AmberTools (http://ambermd.org/AmberTools15-get.html). It provides several clustering algorithms and allows clustering via various metrics (including coordinate RMSD). Hope this helps, -Dan On Tue, Nov 17, 2015 at 4:42 AM, katy emily kellett k.kellett]_[herts.ac.uk wrote: > > Sent to CCL by: "katy emily kellett" [k.kellett+/-herts.ac.uk] > Hi, > > I was wondering if anyone knows of a software or program that can cluster > small molecule conformations from trajectories. I have found a number that > will do it with peptides, but they are not suitable for small molecules, > that I can tell. > > Would appreciate any advice on the topic. > > Thanks very much in advance, > > Katy> > -- ------------------------- Daniel R. Roe, PhD Department of Medicinal Chemistry University of Utah 30 South 2000 East, Room 307 Salt Lake City, UT 84112-5820 http://home.chpc.utah.edu/~cheatham/ (801) 587-9652 (801) 585-6208 (Fax) From owner-chemistry@ccl.net Tue Nov 17 12:47:00 2015 From: "=?UTF-8?Q?Andr=C3=A9_Farias_de_Moura?= moura(-)ufscar.br" To: CCL Subject: CCL: Clustering molecular conformations Message-Id: <-51887-151117084849-15124-DxIN5vXroNNfWZXCVuYnXw|*|server.ccl.net> X-Original-From: =?UTF-8?Q?Andr=C3=A9_Farias_de_Moura?= Content-Type: multipart/alternative; boundary=001a113d1fbcb42af40524bcc8f0 Date: Tue, 17 Nov 2015 11:48:43 -0200 MIME-Version: 1.0 Sent to CCL by: =?UTF-8?Q?Andr=C3=A9_Farias_de_Moura?= [moura(!)ufscar.br] --001a113d1fbcb42af40524bcc8f0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hi Katy, I guess that g_cluster (part of GROMACS suite) can do that for arbitrary molecules, including your so-called small molecules. I hope it helps best Andre On Tue, Nov 17, 2015 at 9:42 AM, katy emily kellett k.kellett]_[herts.ac.uk wrote: > > Sent to CCL by: "katy emily kellett" [k.kellett+/-herts.ac.uk] > Hi, > > I was wondering if anyone knows of a software or program that can cluster > small molecule conformations from trajectories. I have found a number tha= t > will do it with peptides, but they are not suitable for small molecules, > that I can tell. > > Would appreciate any advice on the topic. > > Thanks very much in advance, > > Katy > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 _____________ Prof. Dr. Andr=C3=A9 Farias de Moura Department of Chemistry Federal University of S=C3=A3o Carlos S=C3=A3o Carlos - Brazil phone: +55-16-3351-8090 --001a113d1fbcb42af40524bcc8f0 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi Katy,

I guess that g_cluster (part o= f GROMACS suite) can do that for arbitrary molecules, including your so-cal= led small molecules.

I hope it helps
best

Andre

On Tue, Nov 17, 2015 at 9:42 AM, = katy emily kellett k.kellett]_[herts.ac.uk <owner-chemistry/a\ccl.net> wrote:

Sent to CCL by: "katy emily kellett" [k.kellett+/-herts.ac.uk]
Hi,

I was wondering if anyone knows of a software or program that can cluster small molecule conformations from trajectories. I have found a number that<= br> will do it with peptides, but they are not suitable for small molecules, that I can tell.

Would appreciate any advice on the topic.

Thanks very much in advance,

Katy



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--
_____________

Prof. Dr. Andr=C3=A9 Farias de Moura
Department of Chemistry
Federal University of S=C3=A3o Carlos
S=C3=A3o Carlos - Brazil
phone: +55-16-3351-8090
--001a113d1fbcb42af40524bcc8f0-- From owner-chemistry@ccl.net Tue Nov 17 13:23:00 2015 From: "Rachelle Bienstock rachelleb1(0)gmail.com" To: CCL Subject: CCL: Clustering molecular conformations Message-Id: <-51888-151117121834-30323-smXrMjw04ds741Ap2/9UAw++server.ccl.net> X-Original-From: Rachelle Bienstock Content-Type: multipart/alternative; boundary=001a1142ede0e001530524bfb61a Date: Tue, 17 Nov 2015 12:18:28 -0500 MIME-Version: 1.0 Sent to CCL by: Rachelle Bienstock [rachelleb1]*[gmail.com] --001a1142ede0e001530524bfb61a Content-Type: text/plain; charset=UTF-8 Katy: If you can save the structures in the directory as separate sdf structure files with coordinates, there are lots of small molecule clustering tools available (some for use within KNIME), such as WEKA ( http://www.cs.waikato.ac.nz/ml/weka/), chemmine , (http://chemmine.ucr.edu/) and there may be other fingerprint clustering methods available within the CDK and RDK toolkits. There is also JKlustor from ChemAxon. Rachelle On Tue, Nov 17, 2015 at 6:42 AM, katy emily kellett k.kellett]_[herts.ac.uk wrote: > > Sent to CCL by: "katy emily kellett" [k.kellett+/-herts.ac.uk] > Hi, > > I was wondering if anyone knows of a software or program that can cluster > small molecule conformations from trajectories. I have found a number that > will do it with peptides, but they are not suitable for small molecules, > that I can tell. > > Would appreciate any advice on the topic. > > Thanks very much in advance, > > Katy> > > --001a1142ede0e001530524bfb61a Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Katy:
If you can save the structures in the d= irectory as separate sdf structure files with coordinates, there are lots o= f small molecule clustering tools available (some for use within KNIME), su= ch as WEKA (http://www.cs.= waikato.ac.nz/ml/weka/), chemmine , (http://chemmine.ucr.edu/)=C2=A0 and there may be other
fin= gerprint clustering methods available within the CDK and RDK toolkits.=C2= =A0 There is also JKlustor from ChemAxon.
Rachelle

On Tue, Nov 17, 2015 at= 6:42 AM, katy emily kellett k.kellett]_[her= ts.ac.uk <owner-chemistry a ccl.net> wrote:

Sent to CCL by: "katy emily kellett" [k.kellett+/-herts.ac.uk]
Hi,

I was wondering if anyone knows of a software or program that can cluster small molecule conformations from trajectories. I have found a number that<= br> will do it with peptides, but they are not suitable for small molecules, that I can tell.

Would appreciate any advice on the topic.

Thanks very much in advance,

Katy



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--001a1142ede0e001530524bfb61a-- From owner-chemistry@ccl.net Tue Nov 17 13:57:01 2015 From: "Michel Petitjean petitjean.chiral : gmail.com" To: CCL Subject: CCL: Clustering molecular conformations Message-Id: <-51889-151117124224-9261-pGDiVp1ighV498Yf1rQN7w .. server.ccl.net> X-Original-From: Michel Petitjean Content-Type: text/plain; charset=UTF-8 Date: Tue, 17 Nov 2015 18:42:17 +0100 MIME-Version: 1.0 Sent to CCL by: Michel Petitjean [petitjean.chiral*o*gmail.com] Yes DIVCF computes the number and the sizes of the clusters. If you want to fix the number of clusters yourself, any kind of hierarchical ascending classification should work (look at "R"), then just cut the dendrogram where you like). Best, Michel. Michel Petitjean MTi, INSERM UMR-S 973, University Paris 7, 35 rue Helene Brion, 75205 Paris Cedex 13, France. Phone: +331 5727 8434; Fax: +331 5727 8372 E-mail: petitjean.chiral(_)gmail.com (preferred), michel.petitjean(_)univ-paris-diderot.fr http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html 2015-11-17 14:32 GMT+01:00 Shahar Keinan skeinan%a%gmail.com : > > Sent to CCL by: Shahar Keinan [skeinan.:.gmail.com] > DIVCF from Michel Petitjean can do this: > http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#DIVCF > > The problem is that you can't control the number/size of clusters. > Best, > Shahar > > > On 11/17/15 6:42 AM, katy emily kellett k.kellett]_[herts.ac.uk wrote: >> >> Sent to CCL by: "katy emily kellett" [k.kellett+/-herts.ac.uk] >> Hi, >> >> I was wondering if anyone knows of a software or program that can cluster small molecule conformations from trajectories. I have found a number that >> will do it with peptides, but they are not suitable for small molecules, that I can tell. >> >> Would appreciate any advice on the topic. >> >> Thanks very much in advance, >> >> Katy> >> > > -- > ------------------------------------------------------ > Shahar Keinan > (919) 357 5319 > > From owner-chemistry@ccl.net Tue Nov 17 14:32:00 2015 From: "Arthur Zalevsky aozalevsky(-)gmail.com" To: CCL Subject: CCL: Clustering molecular conformations Message-Id: <-51890-151117141316-13061-ddSxoxPvFUUPAag9Kky0Kg-$-server.ccl.net> X-Original-From: Arthur Zalevsky Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset="utf-8" Date: Tue, 17 Nov 2015 22:13:00 +0300 MIME-Version: 1.0 Sent to CCL by: Arthur Zalevsky [aozalevsky[a]gmail.com] =
I can share my inhouse pipeline based on rmsd and affinity prop= agation clustering algorithm. Also msmbuilder, I think, can do that. <= /div>

From my experience g_cluster produces quite strange r= esults.

Regards,
Arthur

<= div style=3D"width: 100%; font-size: initial; font-family: Calibri, 'Slate = Pro', sans-serif, sans-serif; color: rgb(31, 73, 125); text-align: initial;= background-color: rgb(255, 255, 255);">
= =
<= br style=3D"display:initial">
= = =
= = =
From: Andr=C3=A9 Farias = de Moura moura(-)ufscar.br
Sent: =D0=B2=D1=82=D0=BE=D1=80= =D0=BD=D0=B8=D0=BA, 17 =D0=BD=D0=BE=D1=8F=D0=B1=D1=80=D1=8F 2015 =D0= =B3., 22:04
To: Zalevsky, Arthur
Rep= ly To: CCL Subscribers
Subject: CCL: Clustering molecu= lar conformations

Hi Katy,

I guess that g_cluster (part of GROMAC= S suite) can do that for arbitrary molecules, including your so-called smal= l molecules.

I hope it helps

<= div>best

Andre

On Tue, Nov 17, 2015 at 9:42 AM, katy emi= ly kellett k.kellett]_[herts.ac.uk <owner-chemistry|*|ccl.net> wrote:

Sent to CCL by: "katy emily kellett" [k.kellett+/-herts.ac.uk]
Hi,

I was wondering if anyone knows of a software or program that can cluster small molecule conformations from trajectories. I have found a number that<= br> will do it with peptides, but they are not suitable for small molecules,
that I can tell.

Would appreciate any advice on the topic.

Thanks very much in advance,

Katy



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY|*|c= cl.net or use:
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=
--
_____________

Prof. Dr. Andr=C3=A9 Farias de Moura
Department of Chemistry
Federal University of S=C3=A3o Carlos
S=C3=A3o Carlos - Brazil
phone: +55-16-3351-8090

From owner-chemistry@ccl.net Tue Nov 17 16:19:01 2015 From: "Kellett, Kathryn k.kellett||herts.ac.uk" To: CCL Subject: CCL: Clustering molecular conformations Message-Id: <-51891-151117155234-7465-ZqJedmwXfc7pMRETJRlgRA++server.ccl.net> X-Original-From: "Kellett, Kathryn" Content-Language: en-GB Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 17 Nov 2015 20:52:08 +0000 MIME-Version: 1.0 Sent to CCL by: "Kellett, Kathryn" [k.kellett : herts.ac.uk] Hi all, Thanks so much for all the help and suggestions with the clustering. Have loads of things to try now! Katy > On 17 Nov 2015, at 20:39, Michel Petitjean petitjean.chiral : gmail.com wrote: > > > Sent to CCL by: Michel Petitjean [petitjean.chiral*o*gmail.com] > Yes DIVCF computes the number and the sizes of the clusters. > If you want to fix the number of clusters yourself, any kind of > hierarchical ascending classification should work (look at "R"), then > just cut the dendrogram where you like). > Best, > Michel. > > Michel Petitjean > MTi, INSERM UMR-S 973, University Paris 7, > 35 rue Helene Brion, 75205 Paris Cedex 13, France. > Phone: +331 5727 8434; Fax: +331 5727 8372 > E-mail: petitjean.chiral++gmail.com (preferred), > michel.petitjean++univ-paris-diderot.fr > http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html > > > 2015-11-17 14:32 GMT+01:00 Shahar Keinan skeinan%a%gmail.com > : >> >> Sent to CCL by: Shahar Keinan [skeinan.:.gmail.com] >> DIVCF from Michel Petitjean can do this: >> http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#DIVCF >> >> The problem is that you can't control the number/size of clusters. >> Best, >> Shahar >> >> >>> On 11/17/15 6:42 AM, katy emily kellett k.kellett]_[herts.ac.uk wrote: >>> >>> Sent to CCL by: "katy emily kellett" [k.kellett+/-herts.ac.uk] >>> Hi, >>> >>> I was wondering if anyone knows of a software or program that can cluster small molecule conformations from trajectories. I have found a number that >>> will do it with peptides, but they are not suitable for small molecules, that I can tell. >>> >>> Would appreciate any advice on the topic. >>> >>> Thanks very much in advance, >>> >>> Katy> >> >> -- >> ------------------------------------------------------ >> Shahar Keinan >> (919) 357 5319> > From owner-chemistry@ccl.net Tue Nov 17 16:53:00 2015 From: "Mezei, Mihaly mihaly.mezei[#]mssm.edu" To: CCL Subject: CCL: Clustering molecular conformations Message-Id: <-51892-151117163849-9659-SOlhkB9P9WCppU8pgEe8Qw%server.ccl.net> X-Original-From: "Mezei, Mihaly" Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_23B1335F43764D4EBFA3AC5C9FB1D10BF767FF1CEXCHMBXEB4ExchM_" Date: Tue, 17 Nov 2015 21:38:16 +0000 MIME-Version: 1.0 Sent to CCL by: "Mezei, Mihaly" [mihaly.mezei:-:mssm.edu] --_000_23B1335F43764D4EBFA3AC5C9FB1D10BF767FF1CEXCHMBXEB4ExchM_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Greetings, my program Simulaid (http://inka.mssm.edu/~mezei/simulaid) can cluster fram= es of a trajectory, comparing user-selected parts (with or without superimp= osition) using single-link or k-means clustering. Mihaly Mezei Department of Structural and Chemical Biology, Icahn School of Medicine at = Mount Sinai Voice: (212) 659-5475 Fax: (212) 849-2456 WWW (MSSM home): http://www.mountsinai.org/Find%20A%20Faculty/profile.do?id= =3D0000072500001497192632 WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei WWW (Department): http://www.mssm.edu/departments-and-institutes/structural= -and-chemical-biology --_000_23B1335F43764D4EBFA3AC5C9FB1D10BF767FF1CEXCHMBXEB4ExchM_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
 Greetings,

my program Simulaid (http://inka.mssm.edu/~mezei/simulaid) can cluster frames o= f a trajectory, comparing user-selected parts (with or without superimposit= ion) using single-link or k-means clustering.
Mihaly Mezei

Department of Structural and Chemical Biology, Ica=
hn School of Medicine at Mount Sinai
Voice:  (212) 659-5475   Fax: (212)=
 849-2456
WWW (MSSM home): http://www.mountsinai.org/Find%20A%20Faculty/profile.do?id=3D000007=
2500001497192632
WWW (Lab home - software, publications): http://in=
ka.mssm.edu/~mezei
WWW (Department): http://www.mssm.edu/departments=
-and-institutes/structural-and-chemical-biology

--_000_23B1335F43764D4EBFA3AC5C9FB1D10BF767FF1CEXCHMBXEB4ExchM_-- From owner-chemistry@ccl.net Tue Nov 17 22:13:00 2015 From: "Radhika Narayanan Nair radhika.narayanan.n]=[gmail.com" To: CCL Subject: CCL:G: Optimization with mixture of two solvents using PCM in gaussian Message-Id: <-51893-151117221218-16210-0liNHFWZWizZ2h0eC3Biwg#,#server.ccl.net> X-Original-From: "Radhika Narayanan Nair" Date: Tue, 17 Nov 2015 22:12:17 -0500 Sent to CCL by: "Radhika Narayanan Nair" [radhika.narayanan.n+*+gmail.com] Dear all Could anyone suggest how to carry out the optimization of a metal complex with a mixture of two solvents using polar continuum model (PCM) in Gaussian 09. Thanks Radhika From owner-chemistry@ccl.net Tue Nov 17 23:39:01 2015 From: "Abid Ali abid_channa04!=!yahoo.com" To: CCL Subject: CCL: Cluster conformations Message-Id: <-51894-151117231558-12572-n006ofG+K5qW+zu613JYww,server.ccl.net> X-Original-From: "Abid Ali" Date: Tue, 17 Nov 2015 23:15:56 -0500 Sent to CCL by: "Abid Ali" [abid_channa04]|[yahoo.com] Hi all, g_cluster -h easily available in gromacs utilities gmx cluster can cluster structures using several different methods. Distances between structures can be determined from a trajectory or read from an .xpm matrix file with the -dm option. RMS deviation after fitting or RMS deviation of atom-pair distances can be used to define the distance between structures. Abid Ali Channa, Junior Research Fellow, Lab No. P-133, Computational Chemistry Unit, Dr .Panjwani Center for Molecular Medicine and Drug Research (PCMD), International Center for Chemical and Biological Sciences (ICCBS), University of Karachi-75270.Karachi-Pakistan. UAN # (92-21) 111-222-292 Ext. (309) Cell # +923013553051. http://www.iccs.edu/