From owner-chemistry@ccl.net Thu Sep 29 00:03:00 2011 From: "Andreas W Goetz agoetz[]sdsc.edu" To: CCL Subject: CCL: Survey Request - 10 minutes to help with future AMBER developments Message-Id: <-45543-110928234821-2551-vIWXtALq11HKvK9kGOehSg=-=server.ccl.net> X-Original-From: "Andreas W Goetz" Date: Wed, 28 Sep 2011 23:48:17 -0400 Sent to CCL by: "Andreas W Goetz" [agoetz.###.sdsc.edu] Dear Fellow CCLers, We have a small favor to request. Jointly with NVIDIA we have put together a survey about usage of the AMBER Molecular Dynamics Software Package. This is partly to let NVIDIA know the approximate number of people using the GPU version of AMBER, to gather statistics to aid in funding renewal and to get feedback on what users would like prioritized for development. We would be extremely grateful if those of you that have used AMBER at some point could spare 10 minutes of your Free Time(tm) to please complete the survey linked below. We would also appreciate it if you could encourage other people you know to also complete this survey. They don't need to be users of the AMBER GPU code, just users of AMBER at some point. http://surveys.nvidia.com/index.jsp?pi=f7d3e68a3e1b44841571e6ab4ce2f021 Thank you all for your support. As an incentive for filling out the survey NVIDIA have graciously agreed to donate two NVIDIA C2075 GPUs. Everyone who completes the survey will be entered into a free drawing, where two winners will each receive one of these cards. The lucky winners will be announced in a few weeks when we close the survey. All the best Andy (On behalf of the AMBER-GPU Developers) From owner-chemistry@ccl.net Thu Sep 29 00:38:00 2011 From: "Yawen Li yl6c2!^!mail.missouri.edu" To: CCL Subject: CCL: How can I do cluster analysis or similarity analysis Message-Id: <-45544-110928185349-19412-Zth+j6hYDj9Szpw3PNEBUw__server.ccl.net> X-Original-From: "Yawen Li" Date: Wed, 28 Sep 2011 18:53:47 -0400 Sent to CCL by: "Yawen Li" [yl6c2[*]mail.missouri.edu] Hi, all. I did a molecular dynamics simulation with AMBER, and I saved a thousand conformations during this run. I wish to do some cluster analysis, or similarity analysis on the conformations I saved. I think all the conformations can be groups into two main groups, because I see the structure changes from one conformation to the other in the MD simulation. Is there any free software that does this job? Thank you all for your attention, and I appreciate your help. Yawen Li Graduate Student Chemistry department University of Missouri - Columbia E-mail: yl6c2[#]mail.missouri.edu From owner-chemistry@ccl.net Thu Sep 29 03:06:01 2011 From: "Michel Petitjean petitjean.chiral-*-gmail.com" To: CCL Subject: CCL: How can I do cluster analysis or similarity analysis Message-Id: <-45545-110929030427-25770-16wVILViOUP8pmZScsGJ0g]|[server.ccl.net> X-Original-From: Michel Petitjean Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 29 Sep 2011 09:04:14 +0200 MIME-Version: 1.0 Sent to CCL by: Michel Petitjean [petitjean.chiral^_^gmail.com] Dear Yawen Li, Please have a look at DIVCF: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html Best regards, 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.html 2011/9/29 Yawen Li yl6c2!^!mail.missouri.edu : > > Sent to CCL by: "Yawen  Li" [yl6c2[*]mail.missouri.edu] > Hi, all. > >  I did a molecular dynamics simulation with AMBER, and I saved a thousand conformations during this run. I wish to do some cluster analysis, or similarity analysis on the conformations I saved. I think all the conformations can be groups into two main groups, because I see the structure changes from one conformation to the other in the MD simulation. > >  Is there any free software that does this job? > > Thank you all for your attention, and I appreciate your help. > > > Yawen Li > > Graduate Student > Chemistry department > University of Missouri - Columbia > E-mail: yl6c2,mail.missouri.edu > From owner-chemistry@ccl.net Thu Sep 29 03:41:00 2011 From: "Marcin =?iso-8859-2?Q?Kr=F3l?= mykrol~!~cyf-kr.edu.pl" To: CCL Subject: CCL: How can I do cluster analysis or similarity analysis Message-Id: <-45546-110929031125-5082-aP8Iw+DjZD9F2uvTkO85xQ]|[server.ccl.net> X-Original-From: Marcin =?iso-8859-2?Q?Kr=F3l?= Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-2 Date: Thu, 29 Sep 2011 09:11:16 +0200 MIME-Version: 1.0 Sent to CCL by: Marcin =?iso-8859-2?Q?Kr=F3l?= [mykrol.:.cyf-kr.edu.pl] Hi Yawen If you did the simulation in AMBER you can use ptraj program from the AMBER suite. Have a look at 'cluster' command in ptraj, described in detail in AmberTools manual (http://ambermd.org/doc11/AmberTools.pdf) Best marcin > > Sent to CCL by: "Yawen Li" [yl6c2[*]mail.missouri.edu] > Hi, all. > > I did a molecular dynamics simulation with AMBER, and I saved a thousand > conformations during this run. I wish to do some cluster analysis, or > similarity analysis on the conformations I saved. I think all the > conformations can be groups into two main groups, because I see the > structure changes from one conformation to the other in the MD > simulation. > > Is there any free software that does this job? > > Thank you all for your attention, and I appreciate your help. > > > Yawen Li > > Graduate Student > Chemistry department > University of Missouri - Columbia > E-mail: yl6c2,mail.missouri.edu> > > From owner-chemistry@ccl.net Thu Sep 29 04:31:00 2011 From: "Sergio Manzetti sergio.manzetti,gmail.com" To: CCL Subject: CCL: Molecular geometry similiary Message-Id: <-45547-110929042846-7918-c6EHEPHW19INTVPoDCdd4g|-|server.ccl.net> X-Original-From: Sergio Manzetti Content-Type: multipart/alternative; boundary=20cf30780c32903fd004ae104b39 Date: Thu, 29 Sep 2011 10:28:37 +0200 MIME-Version: 1.0 Sent to CCL by: Sergio Manzetti [sergio.manzetti=-=gmail.com] --20cf30780c32903fd004ae104b39 Content-Type: text/plain; charset=ISO-8859-1 Dear CCL. Does someone know of a program that plots the similiary between two molecules in terms of geomtrical shape and features? It doesn't have to include types of bonds etc, but only shape, size and form. Sergio --20cf30780c32903fd004ae104b39 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear CCL.
Does someone know of a program that plots the similiary betwee= n two molecules in terms of geomtrical shape and=A0 features? It doesn'= t have to include types of bonds etc, but only shape, size and form.
Sergio
--20cf30780c32903fd004ae104b39-- From owner-chemistry@ccl.net Thu Sep 29 05:31:01 2011 From: "Michel Petitjean petitjean.chiral++gmail.com" To: CCL Subject: CCL: Molecular geometry similiary Message-Id: <-45548-110929052904-12429-RyhGKDb5O7QGC/0mkpNvdw+/-server.ccl.net> X-Original-From: Michel Petitjean Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 29 Sep 2011 11:28:53 +0200 MIME-Version: 1.0 Sent to CCL by: Michel Petitjean [petitjean.chiral**gmail.com] Dear Sergio, If the maximal common 3D motif is of interest to you, please have a look at CSR (also performs an optimal superposition): http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html Best regards, 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.html 2011/9/29 Sergio Manzetti sergio.manzetti,gmail.com : > Dear CCL. > Does someone know of a program that plots the similiary between two > molecules in terms of geomtrical shape and  features? It doesn't have to > include types of bonds etc, but only shape, size and form. > > Sergio > From owner-chemistry@ccl.net Thu Sep 29 06:05:00 2011 From: "rv sola rvsolo(!)gmail.com" To: CCL Subject: CCL: AUTODOCK error Message-Id: <-45549-110929055053-23404-UOV1ytHJbG0w1/eSRzx0+A!=!server.ccl.net> X-Original-From: "rv sola" Date: Thu, 29 Sep 2011 05:50:49 -0400 Sent to CCL by: "rv sola" [rvsolo]![gmail.com] dear ccl members, i would like to dock a metal complex with DNA. i am using AUTODOCK windows version and i got the following error message while processing the docking. ERROR: Unknown ligand atom type "Cu"; add parameters for it to the parameter library first! if anybody experienced the same problem and possible solution? yours, rv sola From owner-chemistry@ccl.net Thu Sep 29 08:16:00 2011 From: "veerapandian veera.pandi33_-_gmail.com" To: CCL Subject: CCL: Problem in TDDFT Calculation Message-Id: <-45550-110929005418-19567-nI48yTErbUYtcbcbbuPJcQ(_)server.ccl.net> X-Original-From: veerapandian Content-Type: multipart/alternative; boundary=0015174c0bac98b7cf04ae0d4c5b Date: Thu, 29 Sep 2011 10:24:09 +0530 MIME-Version: 1.0 Sent to CCL by: veerapandian [veera.pandi33[A]gmail.com] --0015174c0bac98b7cf04ae0d4c5b Content-Type: text/plain; charset=ISO-8859-1 Dear Huub, Thank you very much for your answer. As you mentioned my mystery is resolved . Cheers veera On Wed, Sep 28, 2011 at 11:29 PM, Van Dam, Hubertus J HubertusJJ.vanDam-,- pnnl.gov wrote: > > Sent to CCL by: "Van Dam, Hubertus J" [HubertusJJ.vanDam[*]pnnl.gov] > Hi Veerapandian, > > The output lists every excitation separately (excitations of alpha > electrons are labeled "A" and beta electrons "B"). Hence the excitation 97A > -> 99A contributes only once and not twice. So adapting your description you > should use the formula C^2*100 which gives you approximately 61% and your > mystery is resolved. > > Best wishes, > > Huub > > -----Original Message----- > > From: owner-chemistry+hubertus.vandam==pnnl.gov|ccl.net [mailto: > owner-chemistry+hubertus.vandam==pnnl.gov|ccl.net] On Behalf Of veera > pandian ponnuchamy veera.pandi33 ~~ gmail.com > Sent: Tuesday, September 27, 2011 10:44 PM > To: Van Dam, Hubertus J > Subject: CCL: Problem in TDDFT Calculation > > > Sent to CCL by: "veera pandian ponnuchamy" [veera.pandi33()gmail.com] > Hi CCLrs, > I have experienced a surprise case, while calculating the percentage > of contribution in TDDFT calculation. > > This is the output > > Excited State 1: 2.066-A 1.1028 eV 1124.31 nm f=0.0003 > =0.817 > 97B -> 98B 0.99625 > This state for optimization and/or second-order correction. > Total Energy, E(TD-HF/TD-KS) = -1221.52573888 > Copying the excited state density for this state as the 1-particle RhoCI > density. > > Excited State 2: 2.073-A 2.0309 eV 610.49 nm f=0.0003 > =0.825 > 96B -> 98B 0.98993 > > Excited State 3: 3.476-A 2.0710 eV 598.68 nm f=0.0000 > =2.771 > 95A ->103A 0.10782 > 96A ->102A -0.11015 > 98A ->100A 0.68284 > 94B ->105B -0.10218 > 95B ->103B -0.11202 > 96B ->101B 0.11454 > 97B ->100B -0.68191 > 98A <-100A 0.11802 > 97B <-100B -0.11806 > > Excited State 4: 2.852-A 2.5895 eV 478.80 nm f=0.0021 > =1.783 > 98A -> 99A 0.99481 > > Excited State 5: 2.171-A 2.6627 eV 465.63 nm f=0.0193 > =0.928 > 97A -> 99A 0.77986 > 97A ->104A 0.12398 > 90B -> 98B -0.25513 > 92B -> 98B 0.47858 > 93B -> 98B -0.13269 > 95B -> 98B -0.15685 > > > The above state (excited state 5) is the most probable excited state, here > when I calculate the percentage of contribution using C^2*2*100 formula. I > get 121% how it is possible? or am I doing anything wrong? Your help will be > appreciated. > > Thanks in advance... > > Yours > Veerapandian.Phttp:// > www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt> > > -- *Veerapandian.P* School of Chemistry, Bharathidasan University, Tiruchirappalli-620024. --0015174c0bac98b7cf04ae0d4c5b Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Huub,
=A0=A0=A0=A0=A0 Thank you very much for your answer. As you m= entioned my mystery is resolved .

Cheers
veera

On Wed, Sep 28, 2011 at 11:29 PM, Van Dam, Hubertus J Hube= rtusJJ.vanDam-,-pnnl.gov = <owner-chemistry:ccl.net&= gt; wrote:

Sent to CCL by: "Van Dam, Hubertus J" [HubertusJJ.vanDam[*]pnnl.gov]
Hi Veerapandian,

The output lists every excitation separately (excitations of alpha electron= s are labeled "A" and beta electrons "B"). Hence the ex= citation 97A -> 99A contributes only once and not twice. So adapting you= r description you should use the formula C^2*100 which gives you approximat= ely 61% and your mystery is resolved.

Best wishes,

=A0 =A0 =A0Huub

-----Original Message-----
> From: owner-chemistry+hubertus.vandam=3D=3Dpnnl.gov|ccl.net [mailto:= owner-chemistry+hubertus.vandam=3D=3Dpnnl.gov|ccl.n= et] On Behalf Of veera pandian ponnuchamy veera.pandi33 ~~ gmail.com
Sent: Tuesday, September 27, 2011 10:44 PM
To: Van Dam, Hubertus J
Subject: CCL: Problem in TDDFT Calculation


Sent to CCL by: "veera pandian ponnuchamy" [veera.pandi33()gmail.com]
Hi CCLrs,
=A0 =A0 =A0 =A0I have experienced a surprise case, while calculating the p= ercentage of contribution in TDDFT calculation.

This is the output

Excited State =A0 1: =A02.066-A =A0 =A0 =A01.1028 eV 1124.31 nm =A0f=3D0.00= 03 =A0<S**2>=3D0.817
=A0 =A0 97B -> 98B =A0 =A0 =A0 =A00.99625
=A0This state for optimization and/or second-order correction.
=A0Total Energy, E(TD-HF/TD-KS) =3D =A0-1221.52573888
=A0Copying the excited state density for this state as the 1-particle RhoCI= density.

=A0Excited State =A0 2: =A02.073-A =A0 =A0 =A02.0309 eV =A0610.49 nm =A0f= =3D0.0003 =A0<S**2>=3D0.825
=A0 =A0 96B -> 98B =A0 =A0 =A0 =A00.98993

=A0Excited State =A0 3: =A03.476-A =A0 =A0 =A02.0710 eV =A0598.68 nm =A0f= =3D0.0000 =A0<S**2>=3D2.771
=A0 =A0 95A ->103A =A0 =A0 =A0 =A00.10782
=A0 =A0 96A ->102A =A0 =A0 =A0 -0.11015
=A0 =A0 98A ->100A =A0 =A0 =A0 =A00.68284
=A0 =A0 94B ->105B =A0 =A0 =A0 -0.10218
=A0 =A0 95B ->103B =A0 =A0 =A0 -0.11202
=A0 =A0 96B ->101B =A0 =A0 =A0 =A00.11454
=A0 =A0 97B ->100B =A0 =A0 =A0 -0.68191
=A0 =A0 98A <-100A =A0 =A0 =A0 =A00.11802
=A0 =A0 97B <-100B =A0 =A0 =A0 -0.11806

=A0Excited State =A0 4: =A02.852-A =A0 =A0 =A02.5895 eV =A0478.80 nm =A0f= =3D0.0021 =A0<S**2>=3D1.783
=A0 =A0 98A -> 99A =A0 =A0 =A0 =A00.99481

=A0Excited State =A0 5: =A02.171-A =A0 =A0 =A02.6627 eV =A0465.63 nm =A0f= =3D0.0193 =A0<S**2>=3D0.928
=A0 =A0 97A -> 99A =A0 =A0 =A0 =A00.77986
=A0 =A0 97A ->104A =A0 =A0 =A0 =A00.12398
=A0 =A0 90B -> 98B =A0 =A0 =A0 -0.25513
=A0 =A0 92B -> 98B =A0 =A0 =A0 =A00.47858
=A0 =A0 93B -> 98B =A0 =A0 =A0 -0.13269
=A0 =A0 95B -> 98B =A0 =A0 =A0 -0.15685


The above state (excited state 5) is the most probable excited state, here = when I calculate the percentage of contribution using C^2*2*100 formula. I = get 121% how it is possible? or am I doing anything wrong? Your help will b= e appreciated.

Thanks in advance...

Yours
Veerapandian.Phttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.= ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt


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--
Veerapandian.P
School of Chemistry,
Bharathidasan University,
Tiruchir= appalli-620024.



--0015174c0bac98b7cf04ae0d4c5b-- From owner-chemistry@ccl.net Thu Sep 29 08:51:00 2011 From: "Thomas Cheatham tec3*o*utah.edu" To: CCL Subject: CCL: How can I do cluster analysis or similarity analysis Message-Id: <-45551-110929013316-25268-5s0h/w8IAthsSxOVBjp/GQ++server.ccl.net> X-Original-From: Thomas Cheatham Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Wed, 28 Sep 2011 23:33:09 -0600 (Mountain Daylight Time) MIME-Version: 1.0 Sent to CCL by: Thomas Cheatham [tec3-#-utah.edu] > I did a molecular dynamics simulation with AMBER, and I saved a > thousand conformations during this run. I wish to do some cluster > analysis, or similarity analysis on the conformations I saved. I think > all the conformations can be groups into two main groups, because I see > the structure changes from one conformation to the other in the MD > simulation. AMBER has an active mailing list and an archive at http://ambermd.org which would be a good place to search/ask about MD simulations with AMBER. With the freely available AmberTools suite of programs are trajectory analysis capabilities to do clustering. I am most familiar with ptraj which can cluster based on RMSd, distance-matrix, dihedrals, etc. Routinely we cluster based on RMSd. There are many options, but a basic script to ptraj would be something like: trajin traj.strip cluster out clusters/c10 all none representative pdb average pdb \ averagelinkage sieve 250 clusters 10 rms In your case, you can cluster all frames (sieve 1) and to decide on the number of clusters I would visualize a 2D RMSd plot since 1D-RMSd plots can be deceptive with respect to cluster count. See the manuals at http://ambermd.org for more information. A paper describing that implementation is Shao et al. (Cheatham), JCTC ~2007. Alternatives include MMTSB, tools distributed with GROMACS and GROMOS, and likely things builtin to NAMD and CHARMM. If you get stuck, e-mail me off-list. --tec3 From owner-chemistry@ccl.net Thu Sep 29 09:26:01 2011 From: "Iain Moal Iain.Moal.:.cancer.org.uk" To: CCL Subject: CCL: How can I do cluster analysis or similarity analysis Message-Id: <-45552-110929023618-14286-Eb/uImp1s5tFeD/dUP9sFA]![server.ccl.net> X-Original-From: Iain Moal Content-Language: en-GB Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 29 Sep 2011 07:35:31 +0100 MIME-Version: 1.0 Sent to CCL by: Iain Moal [Iain.Moal#,#cancer.org.uk] Hi Yawen, Clustering analysis with AMBER can be found in section 6 of the AMBER tutorial B3: http://ambermd.org/tutorials/ Alternatively, you can use the g_cluster, which comes packaged with the GROMACS. Iain Moal ________________________________________ > From: owner-chemistry+iain.moal==cancer.org.uk_+_ccl.net [owner-chemistry+iain.moal==cancer.org.uk_+_ccl.net] On Behalf Of Yawen Li yl6c2!^!mail.missouri.edu [owner-chemistry_+_ccl.net] Sent: 28 September 2011 23:53 To: Iain Moal Subject: CCL: How can I do cluster analysis or similarity analysis Sent to CCL by: "Yawen Li" [yl6c2[*]mail.missouri.edu] Hi, all. I did a molecular dynamics simulation with AMBER, and I saved a thousand conformations during this run. I wish to do some cluster analysis, or similarity analysis on the conformations I saved. I think all the conformations can be groups into two main groups, because I see the structure changes from one conformation to the other in the MD simulation. Is there any free software that does this job? Thank you all for your attention, and I appreciate your help. Yawen Li Graduate Student Chemistry department University of Missouri - Columbia E-mail: yl6c2,mail.missouri.eduhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtNOTICE AND DISCLAIMER This e-mail (including any attachments) is intended for the above-named person(s). If you are not the intended recipient, notify the sender immediately, delete this email from your system and do not disclose or use for any purpose. We may monitor all incoming and outgoing emails in line with current legislation. We have taken steps to ensure that this email and attachments are free from any virus, but it remains your responsibility to ensure that viruses do not adversely affect you. Cancer Research UK Registered in England and Wales Company Registered Number: 4325234. Registered Charity Number: 1089464 and Scotland SC041666 Registered Office Address: Angel Building, 407 St John Street, London EC1V 4AD. From owner-chemistry@ccl.net Thu Sep 29 11:56:00 2011 From: "Mihaly Mezei Mihaly.Mezei[#]mssm.edu" To: CCL Subject: CCL: How can I do cluster analysis or similarity analysis Message-Id: <-45553-110929115225-6111-cnNZFYUuqBtatJ7BIzaqNw.@.server.ccl.net> X-Original-From: Mihaly Mezei Content-disposition: inline Content-language: en Content-transfer-encoding: 7BIT Content-type: text/plain; charset=us-ascii Date: Thu, 29 Sep 2011 11:51:50 -0400 MIME-version: 1.0 Sent to CCL by: Mihaly Mezei [Mihaly.Mezei##mssm.edu] Greetings, My program Simulaid (http://inka.mssm.edu/~mezei/simulaid) has three different clustering algoritm implemented. Mihaly Mezei Department of Structural and Chemical Biology, Mount Sinai School of Medicine Voice: (212) 659-5475 Fax: (212) 849-2456 WWW (MSSM home): http://www.mountsinai.org/Find%20A%20Faculty/profile.do?id=0000072500001497192632 WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei WWW (Department): http://atlas.physbio.mssm.edu From owner-chemistry@ccl.net Thu Sep 29 14:23:01 2011 From: "Mikko Vainio mikko.vainio|a|abo.fi" To: CCL Subject: CCL: Molecular geometry similiary Message-Id: <-45554-110929122131-712-w/T0JS2maq2/SEAHaMJ5nQ{=}server.ccl.net> X-Original-From: Mikko Vainio Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 29 Sep 2011 18:21:14 +0200 MIME-Version: 1.0 Sent to CCL by: Mikko Vainio [mikko.vainio^^^abo.fi] On 09/29/2011 10:28 AM, Sergio Manzetti sergio.manzetti,gmail.com wrote: > Dear CCL. > Does someone know of a program that plots the similiary between two > molecules in terms of geomtrical shape and features? It doesn't have > to include types of bonds etc, but only shape, size and form. > > Sergio Hi Sergio, ShaEP is a free-of-charge program that can superimpose molecular structures by maximizing their volume overlap. By default, it also takes into account the electrostatic potential of the molecules but that can be turned off. You can download ShaEP for Windows, Linux, Mac, or FreeBSD from http://users.abo.fi/mivainio/shaep/ Cheers, Mikko From owner-chemistry@ccl.net Thu Sep 29 15:32:00 2011 From: "Patrizia Calaminici pcalamin##cinvestav.mx" To: CCL Subject: CCL: How can I do cluster analysis or similarity analysis Message-Id: <-45555-110929120610-14599-IswKAodyLVcrj0lj7gdZkg(0)server.ccl.net> X-Original-From: Patrizia Calaminici Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 29 Sep 2011 16:06:27 +0000 MIME-Version: 1.0 Sent to CCL by: Patrizia Calaminici [pcalamin++cinvestav.mx] Dear Yawen Li, I would like to suggest you to give a look at our reference J.C.P. 131, 124126 (2009). This work presents a quite powerful alignment algorithm which allows to study the structural evolution and to perform the similarity analysis of different geometrical structures along Born-Oppenheimer molecular dynamics simulations. We have implemented this algorithm in the deMon2k code, which is free of charge for academics (http://www.demon-software.com/public_html/index.html). Hopefully this information will be useful for your purpose. Please, do not hesitate to contact me directly over e-mail if interested in further details about. Kind regards, Patrizia Calaminici (_)===================================(_) Prof. Dr. Patrizia Calaminici Departamento de Quimica, CINVESTAV, Centro De Investigacion Y De Estudios Avanzados, Av. Instituto Politecnico Nacional, 2508 A.P. 14-740 Mexico D.F. 07000 MEXICO Tel: 5255-5-747-3911 (Office) 5255-5-747-3800 Ext. 4411, 4465 (Labs) Fax: 5255-5-747-3389 E-mails: pcalamin(_)cinvestav.mx, calaminicipatrizia(_)gmail.com http://www.quimica.cinvestav.mx/Directorio/Investigadores/DraCalaminiciPatrizia.aspx Secretary: Miss. Lorena Sanchez Mendoza Tel: 5255-5-747-3800 Ext. 4408 E-mail: lsmendoza(_)cinvestav.mx (_)=================================(_) ________________________________________ > From: owner-chemistry+pcalamin==cinvestav.mx(_)ccl.net [owner-chemistry+pcalamin==cinvestav.mx(_)ccl.net] on behalf of Yawen Li yl6c2!^!mail.missouri.edu [owner-chemistry(_)ccl.net] Sent: Wednesday, September 28, 2011 5:53 PM To: Patrizia Calaminici Subject: CCL: How can I do cluster analysis or similarity analysis Sent to CCL by: "Yawen Li" [yl6c2[*]mail.missouri.edu] Hi, all. I did a molecular dynamics simulation with AMBER, and I saved a thousand conformations during this run. I wish to do some cluster analysis, or similarity analysis on the conformations I saved. I think all the conformations can be groups into two main groups, because I see the structure changes from one conformation to the other in the MD simulation. Is there any free software that does this job? Thank you all for your attention, and I appreciate your help. Yawen Li Graduate Student Chemistry department University of Missouri - Columbia E-mail: yl6c2,mail.missouri.eduhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt