From owner-chemistry@ccl.net Mon May 11 01:26:01 2009 From: "Rene Thomsen rt[a]molegro.com" To: CCL Subject: CCL: Molegro releases Molegro Virtual Docker 3.2 Message-Id: <-39270-090511011136-20955-9YT69KH90l2DUHdriLtbYQ]|[server.ccl.net> X-Original-From: "Rene Thomsen" Date: Mon, 11 May 2009 01:11:33 -0400 Sent to CCL by: "Rene Thomsen" [rt,+,molegro.com] Aarhus, Denmark, May 11th, 2009 - Molegro is pleased to announce a new release of Molegro Virtual Docker, an integrated platform for computational drug design available for Windows, Linux, and Mac OS X. Molegro Virtual Docker offers high-quality protein-ligand docking based on novel optimization techniques combined with a user interface experience focusing on usability and productivity. New features in version 3.2: * Docking post-processing: it is now possible to perform energy minimization and optimize protein/ligand hydrogen bonds after docking. * The Data Analyzer in MVD has been updated with a new chemistry module. The Data Analyzer is now able to show 2D depictions of molecules and docking results. Molecules may be depicted inside the spreadsheet cells or in a separate grid window. It is also possible to visualize the molecules directly in the 2D plotter and optionally cluster overlapping molecules. * Ligand Energy Inspector has been improved with new options and more detailed energy overview. * Cavities can now be merged and it is possible to restrict cavity detection to a specific region of the protein. * More than 50 other improvements and bug fixes. To download a trial version, please visit our company website at: http://www.molegro.com. For more information contact: Rene Thomsen, CEO Molegro C. F. Moellers Alle 8, Bldg. 1110 DK-8000 Aarhus Denmark E-mail: rt%x%molegro.com Phone: (+45) 89 42 31 65 About Molegro Molegro is a Danish company founded in 2005. Our company concentrates on developing high-performance drug discovery solutions leading to a faster drug-development process. Our goal is to provide scientifically superior products focusing on both state-of-the-art algorithms and an intuitive graphical user interface experience. From owner-chemistry@ccl.net Mon May 11 07:39:00 2009 From: "Rafael R. Pappalardo rafapa : us.es" To: CCL Subject: CCL: Question on gar2ped for PED calculations Message-Id: <-39271-090511073201-30692-wZMpPNIqtmPN3Uli7kRgeA##server.ccl.net> X-Original-From: "Rafael R. Pappalardo" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: multipart/alternative; boundary="Boundary-00=_DKACKi9I69zm261" Date: Mon, 11 May 2009 12:48:35 +0200 MIME-Version: 1.0 Sent to CCL by: "Rafael R. Pappalardo" [rafapa!=!us.es] --Boundary-00=_DKACKi9I69zm261 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit On Sunday 10 May 2009 04:23:32 Sulayman Oladepo soladepo[-]ualberta.ca wrote: > Sent to CCL by: "Sulayman Oladepo" [soladepo[*]ualberta.ca] > Hi, > I am mailing to ask a question about the gar2ped program. I got information > from that this program could be downloaded from the CCL website. I have > downloaded the program, but for some reasons it doesn't work. I know some > former members of my reserach group had successfully used it for PED > calculations in the past. But for quite some time now, even those who had > used it in the past cann't get it to work. I just tried downloading the > program again, using a munual written by a former group member as a guide. > But it still didn't work. I'm wondering there must be something missing to > get it to work. Can you please offer some suggestions about how to get this > program to work? Any suggestions about other programs that can do similar > calculations as gar2ped will be appreciated. Basically, i need a program > that can give internal coordinates as well as as potential energy > distribution (PED) information just like gar2ped. Thank you. > > Sulayman Oladepo > soladepo]*[ualberta.caDear Sir, could you be more specific about which kind of error are you getting? What's the compiler, operating system, input file, etc. I have been able to use gar2ped a lot of time ago, maybe I could help if you send me the details. Best regards, Rafael -- Dr. Rafael R. Pappalardo Physical Chemistry Dept., Univ. de Sevilla (Spain) e-mail: rafapa]^[us.es --Boundary-00=_DKACKi9I69zm261 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: 7bit On Sunday 10 May 2009 04:23:32 Sulayman Oladepo soladepo[-]ualberta.ca wrote:
> Sent to CCL by: "Sulayman Oladepo" [soladepo[*]ualberta.ca]
> Hi,
> I am mailing to ask a question about the gar2ped program. I got information
> from that this program could be downloaded from the CCL website. I have
> downloaded the program, but for some reasons it doesn't work. I know some
> former members of my reserach group had successfully used it for PED
> calculations in the past. But for quite some time now, even those who had
> used it in the past cann't get it to work. I just tried downloading the
> program again, using a munual written by a former group member as a guide.
> But it still didn't work. I'm wondering there must be something missing to
> get it to work. Can you please offer some suggestions about how to get this
> program to work? Any suggestions about other programs that can do similar
> calculations as gar2ped will be appreciated. Basically, i need a program
> that can give internal coordinates as well as as potential energy
> distribution (PED) information just like gar2ped. Thank you.
>
> Sulayman Oladepo
> soladepo]*[ualberta.ca
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> Subscribe/Unsubscribe:
>
>
>
>
> Job: http://www.ccl.net/jobs
>
>
>
>
>
>
>
>
Dear Sir,
could you be more specific about which kind of error are you getting? What's the compiler, operating system, input file, etc.
I have been able to use gar2ped a lot of time ago, maybe I could help if you send me the details.


Best regards,


Rafael
--
Dr. Rafael R. Pappalardo
Physical Chemistry Dept., Univ. de Sevilla (Spain)
e-mail: rafapa]^[us.es

--Boundary-00=_DKACKi9I69zm261-- From owner-chemistry@ccl.net Mon May 11 09:16:00 2009 From: "David Marlanov davma7-,-gmail.com" To: CCL Subject: CCL:G: Global geometry optimization Message-Id: <-39272-090511055535-26948-CE/tPBtwoDgvFNSwERF6Pw**server.ccl.net> X-Original-From: "David Marlanov" Date: Mon, 11 May 2009 05:55:31 -0400 Sent to CCL by: "David Marlanov" [davma7]|[gmail.com] Dear colleagues! I'm not professional in quantum chemistry. I did local optimization in g03 and gamess (us) many times. As I understood global geometry optimization (finding the geometry with global energy minimum) was not implemented in these programs ( I mean Monte Carlo methods, genetic algorithm, etc.). Is there any program in quantum chemistry that can do such kind of optimization? I browsed the net and found many articles about this topic but not implemented algorithm. Thanks a lot! From owner-chemistry@ccl.net Mon May 11 09:50:00 2009 From: "Kamel Mansouri kamel_mansouri*_*yahoo.fr" To: CCL Subject: CCL: sybyl conformers Message-Id: <-39273-090511085724-29591-AxwW0lPcefvwQOuucvsVgg%a%server.ccl.net> X-Original-From: Kamel Mansouri Content-Type: multipart/alternative; boundary="0-908076956-1242043032=:31941" Date: Mon, 11 May 2009 11:57:12 +0000 (GMT) MIME-Version: 1.0 Sent to CCL by: Kamel Mansouri [kamel_mansouri-#-yahoo.fr] --0-908076956-1242043032=:31941 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Dear all,=0A=0AI'm tryin to make a comparison between different free and pa= id conformer generators, but for Sybyl Tripos I'm still looking in differen= t docs but I can't find information about if ring conformations can be requ= ested.=0APlease help me to be sure about that, and every other interesting = detail is welcome.=0A=0AThanks =0A=0A=0A=0A --0-908076956-1242043032=:31941 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
Dear all,

I'm tryin to make a comparison between different f= ree and paid conformer generators, but for Sybyl Tripos I'm still looking i= n different docs but I can't find information about if ring conformations c= an be requested.
Please help me to be sure about that, and every other i= nteresting detail is welcome.

Thanks

=0A=0A=0A= =0A --0-908076956-1242043032=:31941-- From owner-chemistry@ccl.net Mon May 11 10:26:01 2009 From: "Saurabh Agrawal Saurabh.Agrawal^_^ucdconnect.ie" To: CCL Subject: CCL: free docking Message-Id: <-39274-090511083124-24317-ZrLmDcMZjY0vZYu6Ha7ppw]~[server.ccl.net> X-Original-From: Saurabh Agrawal Content-language: en Content-type: multipart/alternative; boundary="Boundary_(ID_D1camAoNAR1zChu7Q8Z2bA)" Date: Mon, 11 May 2009 12:22:39 +0100 MIME-version: 1.0 Sent to CCL by: Saurabh Agrawal [Saurabh.Agrawal/./ucdconnect.ie] This is a multi-part message in MIME format. --Boundary_(ID_D1camAoNAR1zChu7Q8Z2bA) Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: QUOTED-PRINTABLE Content-disposition: inline Hello, Dock is a free software and could be useful for you. http://dock.compbio.ucsf.edu/ Cheers, Saurabh ----- Original Message ----- =46rom: "Jacopo=A0Sgrignani=A0sgrigna]|[gmail.com" Date: Friday, May 8, 2009 5:28 pm Subject: CCL: free docking To: "Agrawal, Saurabh=A0" > Dear all > can anybody suggest me a free (for academics) docking software. I'm= using autodock=A0but=20 > i have problem of docking accuracy on the system i'm=A0studying. > I would like to try another software, if possible with a GUI=A0to s= etup the calculation. =20 > Thanks in advance > Jacopo=A0 =20 Saurabh=A0Agrawal, PhD Student, Department of Chemical and Bioprocess=A0Engineering, UCD, Belfield, Dublin-4, Ireland --Boundary_(ID_D1camAoNAR1zChu7Q8Z2bA) Content-type: text/html; charset=us-ascii Content-transfer-encoding: QUOTED-PRINTABLE Content-disposition: inline Hello,

Dock is a free software and could be useful for you.
http://dock.compbio.ucsf.edu/

Cheers,

Saurabh
<= br>
----- Original Message -----
From: "Jacopo Sgrignani&n= bsp;sgrigna]|[gmail.com" <owner-chemistry##ccl.net>
Date: Fri= day, May 8, 2009 5:28 pm
Subject: CCL: free docking
To: "Agrawa= l, Saurabh " <Saurabh.Agrawal##ucdconnect.ie>
> Dear all
= > can anybody su= ggest me a free (for academics) docking software. I'm using autodock&= nbsp;but
> i= have problem of docking accuracy on the system i'm studying.> I would like = to try another software, if possible with a GUI to setup the cal= culation.

> Thanks in advance

> Jacopo 


Saurabh Agrawal,
PhD = Student,
Department of Chemical and Bioprocess Engineering,UCD, Belfield,
Dublin-4, Ireland
--Boundary_(ID_D1camAoNAR1zChu7Q8Z2bA)-- From owner-chemistry@ccl.net Mon May 11 11:01:01 2009 From: "Marcel Swart marcel.swart/./icrea.es" To: CCL Subject: CCL:G: Global geometry optimization Message-Id: <-39275-090511102030-7402-vOmPpP6GxNqDAzwcAwuqhw . server.ccl.net> X-Original-From: Marcel Swart Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Mon, 11 May 2009 16:16:39 +0200 MIME-Version: 1.0 Sent to CCL by: Marcel Swart [marcel.swart|a|icrea.es] No, I don't think so. This is because quantum-chemistry is so time-consuming that it often is worthwhile to use human intelligence (aka chemical intuition). So, what you could do is generate a number of different conformations (I'm assuming here that you have a floppy molecule) at a low-level (MM or semi-empircal), and then reoptimize at a higher-level QM. I've used Spartan in the past, and that program did have such an option. Quoting "David Marlanov davma7-,-gmail.com" : > > Sent to CCL by: "David Marlanov" [davma7]|[gmail.com] > Dear colleagues! > I'm not professional in quantum chemistry. > I did local optimization in g03 and gamess (us) many times. As I =20 > understood global geometry optimization (finding the geometry with =20 > global energy minimum) was not implemented in these programs ( I =20 > mean Monte Carlo methods, genetic algorithm, etc.). Is there any =20 > program in quantum chemistry that can do such kind of optimization? > I browsed the net and found many articles about this topic but not =20 > implemented algorithm. > > Thanks a lot! > > > > -=3D This is automatically added to each message by the mailing script =3D= -> > > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D dr. Marcel Swart ICREA researcher at Institut de Qu=EDmica Computacional Universitat de Girona Parc Cient=EDfic i Tecnol=F2gic Edifici Jaume Casademont (despatx A-27) Pic de Peguera 15 17003 Girona Catalunya (Spain) tel +34-972-183240 fax +34-972-183241 e-mail marcel.swart,icrea.es marcel.swart,udg.edu web http://www.icrea.cat/Web/ScientificForm.aspx?key=3D372 http://iqc.udg.edu/~marcel =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D From owner-chemistry@ccl.net Mon May 11 11:36:01 2009 From: "Alessandro Contini alessandro.contini() unimi.it" To: CCL Subject: CCL:G: Global geometry optimization Message-Id: <-39276-090511104937-30236-Vv8/lDI8lg6si7vU9T00wg++server.ccl.net> X-Original-From: Alessandro Contini Content-transfer-encoding: 8BIT Content-type: text/plain; charset=UTF-8 Date: Mon, 11 May 2009 16:04:13 +0200 MIME-version: 1.0 Sent to CCL by: Alessandro Contini [alessandro.contini||unimi.it] Hi, doing a global optimization by mean of quantum mechanic methods might be very time consuming. Probably it could be better performing a conformational search by molecular mechanics and then perform geometry optimization of all conformers within a certain energy treshold by mean of a quantum chemistry method. Regards, Alessandro Contini Il giorno lun, 11/05/2009 alle 05.55 -0400, David Marlanov davma7-,-gmail.com ha scritto: > Sent to CCL by: "David Marlanov" [davma7]|[gmail.com] > Dear colleagues! > I'm not professional in quantum chemistry. > I did local optimization in g03 and gamess (us) many times. As I understood global geometry optimization (finding the geometry with global energy minimum) was not implemented in these programs ( I mean Monte Carlo methods, genetic algorithm, etc.). Is there any program in quantum chemistry that can do such kind of optimization? > I browsed the net and found many articles about this topic but not implemented algorithm. > > Thanks a lot!> > -- Dr. Alessandro Contini DISMAB - Sezione di Chimica Organica "Alessandro Marchesini" Università degli Studi di Milano Via Venezian, 21 20133 Milano Tel. +390250314480 Fax. +390250314476 e-mail alessandro.contini-$-unimi.it skype alessandrocontini From owner-chemistry@ccl.net Mon May 11 12:11:00 2009 From: "Ekaterina Zueva zueva_ekaterina-.-mail.ru" To: CCL Subject: CCL:G: using Jaguar's orbitals in Gaussian Message-Id: <-39277-090511092112-1019-TxsjKqnMnuDgw0xZrFtrpA a server.ccl.net> X-Original-From: "Ekaterina Zueva" Date: Mon, 11 May 2009 09:21:08 -0400 Sent to CCL by: "Ekaterina Zueva" [zueva_ekaterina\a/mail.ru] Dear All, I tried to use the orbitals generated by Jaguar (writted in *.gau file) in a Gaussian job, but all my attempts were unsuccessful: a Gaussian job terminated with an error "Unable to orthonormalize Vectors". I tried several basis sets (TZV or LACVD), but got the same message from Gaussian. I don't understand the reason of that. I used ip160=4 and ip104=9 in gen section of Jaguar's input file, and made 1 SCF (igonly=1) or a few SCF cycles. The resulting orbitals were used by Gaussian by specifying guess=cards and (in case of LACVD) pseudo=cards. I would be very gratefull if you could give a comment on this. Thank you in advance, Katerina From owner-chemistry@ccl.net Mon May 11 12:48:00 2009 From: "Senthil Natesan sen.natesan]^[yahoo.com" To: CCL Subject: CCL: CRAY CX1 supercomputer experience? Message-Id: <-39278-090511120607-24216-RqaXVAH7qzpJaWbBFc/Wrg*|*server.ccl.net> X-Original-From: "Senthil Natesan" Date: Mon, 11 May 2009 12:06:04 -0400 Sent to CCL by: "Senthil Natesan" [sen.natesan()yahoo.com] Hi, Warm wishes to everyone.. Our group is planning to purchase a new hardware (probably CRAY CX1 supercomputer). We essentially use Sybyl, Schrodinger etc.. I will sincerely appreciate sharing your experience with CRAY CX1, positives and negatives and suggestions before purchasing.. Is there any other brands or combination of features giving superior performances ? My ultimate goal is to get comprehensive idea/recommendations to buy a powerful, hassle-free high performance computer (super-computer ?). Thanks in advance for sharing your valuable experience. Senthil Natesan From owner-chemistry@ccl.net Mon May 11 13:20:00 2009 From: "Eduard Matito ematito^gmail.com" To: CCL Subject: CCL:G: aromacity Message-Id: <-39279-090511121701-32061-myU4G5rXK4vyv5KOuFcYBA]-[server.ccl.net> X-Original-From: Eduard Matito Content-Type: multipart/alternative; boundary=Apple-Mail-51--389405800 Date: Mon, 11 May 2009 18:11:22 +0200 Mime-Version: 1.0 (Apple Message framework v930.3) Sent to CCL by: Eduard Matito [ematito|a|gmail.com] --Apple-Mail-51--389405800 Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Content-Transfer-Encoding: 7bit Hi Patris, NICS is indeed available with gaussian (see keyword NMR in the manual). I'm afraid HOMA, FLU and PDI are not available as a direct output of gaussian. For HOMA you may easily write a small program to calculate its values or even do it by hand; you just need geometry and a set of parameters (see for instance Chem. Rev. 101, 1385). For FLU and PDI you will need gaussian wave function file (check for out=wfn keyword in gaussian). In addition, you need another program to read this file and calculate the atomic overlaps. From these atomic overlap files you can calculate FLU or PDI indices. This program will help in the last step: http://iqc.udg.edu/~eduard/ESI/ There you will also find a manual which explains how to do these calculations, and there are few links to free programs to calculate atomic overlaps. Hope this helps, Eduard On May 10, 2009, at 11:35 AM, patris canary patriscanary-*-gmail.com wrote: > > Sent to CCL by: "patris canary" [patriscanary * gmail.com] > Dear All > I need the knowledge about calculating aromacity indices like homa, > nics, flu pdi and Wiberg bond indices with gaussian 03 keyword or > input and output file for this calculation. > Thanks in advance > Regards... > > > > -= This is automatically added to each message by the mailing script > =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/> > -- Eduard Matito Postdoctoral researcher Institute of Physics University of Szczecin Wielkopolska 15 70451 Szczecin (Poland) --Apple-Mail-51--389405800 Content-Type: text/html; charset=US-ASCII Content-Transfer-Encoding: quoted-printable Hi Patris,
NICS is indeed = available with gaussian (see keyword NMR in the manual). I'm afraid = HOMA, FLU and PDI are not available as a direct output of = gaussian.
For HOMA you may easily write a small program to = calculate its values or even do it by hand; you just need geometry = and a set of parameters (see for instance Chem. Rev. 101, = 1385). 
For FLU and PDI you will need gaussian wave = function file (check for out=3Dwfn keyword in gaussian). In = addition, you need another program to read this file and calculate the = atomic overlaps. =46rom these atomic overlap files you can calculate FLU = or PDI indices.
This program will help in the last = step:

On May 10, 2009, at = 11:35 AM, patris canary patriscanary-*-gmail.com wrote:


Sent to CCL by: "patris   canary" = [patriscanary * gmail.com]
Dear All
I need the knowledge about = calculating aromacity indices like homa, nics, flu  pdi and Wiberg =  bond indices with gaussian 03 keyword or input and output file for = this calculation.
Thanks in advance
Regards...



-=3D = This is automatically added to each message by the mailing script = =3D-
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<= /div>
Institute of = Physics
University of = Szczecin
To: CCL Subject: CCL: How to add missing residues Message-Id: <-39280-090511124944-26170-ePFBa1PPFjdrDf5ZEy1/lA]*[server.ccl.net> X-Original-From: "Sangeetha Vimal" Date: Mon, 11 May 2009 12:49:40 -0400 Sent to CCL by: "Sangeetha Vimal" [srdshigella]^[gmail.com] Hello everyone, Can someone post the tools/methods available for building missing residues in the crystal structure. I need the complete structure for carrying out simulation studies. thanks sangeetha. From owner-chemistry@ccl.net Mon May 11 14:31:01 2009 From: "Paul Hawkins phawkins||eyesopen.com" To: CCL Subject: CCL: free docking Message-Id: <-39281-090508131447-10226-s3MeTf3BJvDvEX8NgB5rVw||server.ccl.net> X-Original-From: Paul Hawkins Content-Language: en-US Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Fri, 8 May 2009 09:42:28 -0700 MIME-Version: 1.0 Sent to CCL by: Paul Hawkins [phawkins_-_eyesopen.com] Jacopo, As an academic you are entitled to use the OpenEye suite for free, which in= cludes the docking engine FRED. You can apply for an academic license at http://www.eyesopen.com/forms/academic_license_app.php Paul. ________________________________________ > From: owner-chemistry+phawkins=3D=3Deyesopen.com _ ccl.net [owner-chemistry+p= hawkins=3D=3Deyesopen.com _ ccl.net] On Behalf Of Jacopo Sgrignani sgrigna]|[= gmail.com [owner-chemistry _ ccl.net] Sent: Friday, May 08, 2009 8:33 AM To: Paul Hawkins Subject: CCL: free docking Dear all can anybody suggest me a free (for academics) docking software. I'm using a= utodock but i have problem of docking accuracy on the system i'm studying. I would like to try another software, if possible with a GUI to setup the c= alculation. Thanks in advance Jacopo From owner-chemistry@ccl.net Mon May 11 15:06:00 2009 From: "amit dong dongamit123[-]gmail.com" To: CCL Subject: CCL: heavy atoms Message-Id: <-39282-090510234358-27742-xBBwPnn+gjcOCqifGi3PHQ###server.ccl.net> X-Original-From: amit dong Content-Type: multipart/alternative; boundary=0016e646a2e4fde75e046999c476 Date: Sun, 10 May 2009 21:31:02 -0500 MIME-Version: 1.0 Sent to CCL by: amit dong [dongamit123{=}gmail.com] --0016e646a2e4fde75e046999c476 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi group! Is there any tool that can calculate the heavy atom count of compounds given a multi-mol2 file? Thanks AD --0016e646a2e4fde75e046999c476 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi group!

Is there any tool that can calculate the heavy atom count of compounds given a multi-mol2 file?

Thanks
AD
--0016e646a2e4fde75e046999c476-- From owner-chemistry@ccl.net Mon May 11 15:43:00 2009 From: "Ugur Mart ugurmart ~~ yahoo.com" To: CCL Subject: CCL: Software suggestion Message-Id: <-39283-090511113243-30619-kdOibE7B+4aZZ2b5t0su8w]-[server.ccl.net> X-Original-From: Ugur Mart Content-Type: multipart/alternative; boundary="0-559936031-1242052348=:42564" Date: Mon, 11 May 2009 07:32:28 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Ugur Mart [ugurmart!=!yahoo.com] --0-559936031-1242052348=:42564 Content-Type: text/plain; charset=us-ascii Can anyone suggest, if available, preferably free software for drawing atomistic models, molecules and building crystal structures and surfaces. Material Studio is I know one of the best but too expensive, isn't it? Best regards Ugur --0-559936031-1242052348=:42564 Content-Type: text/html; charset=us-ascii
Can anyone suggest, if available, preferably free software for drawing atomistic models, molecules and building crystal structures and surfaces.
Material Studio is I know one of the best but too expensive, isn't it? 
Best regards
Ugur

--0-559936031-1242052348=:42564-- From owner-chemistry@ccl.net Mon May 11 16:16:01 2009 From: "Bahareh honarparvar bahareh_honarparvar(-)yahoo.com" To: CCL Subject: CCL:G: Global geometry optimization Message-Id: <-39284-090511112058-21280-WYXd0PHle5xilLBvxRHofA/a\server.ccl.net> X-Original-From: Bahareh honarparvar Content-Type: multipart/alternative; boundary="0-1247764714-1242051643=:31742" Date: Mon, 11 May 2009 07:20:43 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Bahareh honarparvar [bahareh_honarparvar!A!yahoo.com] --0-1247764714-1242051643=:31742 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear David Marlanov , you are right ! g03 and gamess are useful for finding local minima for Global geometry optimization you have to work with simulation programs = such as VASP or charmm. I hope that this answers your question. =0A Good luck =0A=0ABahareh Honarparvar=0A=0A --- On Mon, 5/11/09, David Marlanov davma7-,-gmail.com wrote: > From: David Marlanov davma7-,-gmail.com Subject: CCL:G: Global geometry optimization To: "Honarparvar, Honarparvar " Date: Monday, May 11, 2009, 2:25 PM Sent to CCL by: "David=A0 Marlanov" [davma7]|[gmail.com] Dear colleagues! I'm not professional in quantum chemistry.=20 I did local optimization=A0 in g03 and gamess (us) many times. As I underst= ood global geometry optimization (finding the geometry with global energy m= inimum) was not implemented in these programs ( I mean Monte Carlo methods,= genetic algorithm, etc.). Is there any program in quantum chemistry that c= an do such kind of=A0 optimization? I browsed the net and found many articles about this topic but not implemen= ted algorithm. Thanks a lot! -=3D This is automatically added to each message by the mailing script =3D-=A0 =A0 =A0=A0 =A0 =A0Subscribe/Unsubscribe:=20 =A0 =A0 =A0Job: http://www.ccl.net/jobs=20=A0 =A0 =A0=0A=0A=0A --0-1247764714-1242051643=:31742 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear David Marlanov ,
you are right ! g03 = and gamess are useful for finding local minima
for Global geometry optim= ization you have to work with simulation programs such as VASP or charmm.I hope that this answers your question.=
=0A=
Good luck
=0A=0A

Bahareh Honarparvar=

=0A=0A

= --- On Mon, 5/11/09, David Marlanov davma7-,-gmail.com <owner-chem= istry^ccl.net> wrote:

From: Davi= d Marlanov davma7-,-gmail.com <owner-chemistry^ccl.net>
Subject: C= CL:G: Global geometry optimization
To: "Honarparvar, Honarparvar -id#4wv= -" <bahareh_honarparvar^yahoo.com>
Date: Monday, May 11, 2009, 2:2= 5 PM


Sent to CCL by: "David  Marla= nov" [davma7]|[gmail.com]
Dear colleagues!
I'm not professional in qu= antum chemistry.
I did local optimization  in g03 and gamess (us) = many times. As I understood global geometry optimization (finding the geome= try with global energy minimum) was not implemented in these programs ( I m= ean Monte Carlo methods, genetic algorithm, etc.). Is there any program in = quantum chemistry that can do such kind of  optimization?
I browsed the net and found many articles about this topi= c but not implemented algorithm.

Thanks a lot!



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=0A=0A --0-1247764714-1242051643=:31742-- From owner-chemistry@ccl.net Mon May 11 16:51:01 2009 From: "Rene Fournier renef _ yorku.ca" To: CCL Subject: CCL:G: Global geometry optimization Message-Id: <-39285-090511130515-20870-KXYDU3V9yG1JUuTkZ9qiKQ : server.ccl.net> X-Original-From: Rene Fournier Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Mon, 11 May 2009 12:32:09 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: Rene Fournier [renef=yorku.ca] >Is there any program in quantum chemistry that can do such >kind of optimization? Spartan has had it for many years, but I think it's only for conformation search, ie "bonds" can't be broken or formed during optimization. VASP can do simulated annealing in a general way, I suppose in principle it could work for anything. We used shell scripts to combine our "Taboo Search" code with G03 and VASP and do global optimization at DFT level (see PRA 79 (2009) 043202 and 043203 for recent applications). Ours is a research code still under development --- not user-friendly, not well supported, and only works for clusters --- but if you're interested, let me know. -- Rene Rene Fournier, Chemistry, York University, renef[*]yorku.ca On Mon, 11 May 2009, David Marlanov davma7-,-gmail.com wrote: > > Sent to CCL by: "David Marlanov" [davma7]|[gmail.com] > Dear colleagues! > I'm not professional in quantum chemistry. > I did local optimization in g03 and gamess (us) many times. As I understood global geometry optimization (finding the geometry with global energy minimum) was not implemented in these programs ( I mean Monte Carlo methods, genetic algorithm, etc.). Is there any program in quantum chemistry that can do such kind of optimization? > I browsed the net and found many articles about this topic but not implemented algorithm. > > Thanks a lot!> > > From owner-chemistry@ccl.net Mon May 11 17:25:00 2009 From: "Deepangi Pandit deepangi.pandit\a/gmail.com" To: CCL Subject: CCL: How to add missing residues Message-Id: <-39286-090511153923-15056-luvy3thlPTXSyLK5jlw0Kg * server.ccl.net> X-Original-From: Deepangi Pandit Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 11 May 2009 14:38:26 -0400 MIME-Version: 1.0 Sent to CCL by: Deepangi Pandit [deepangi.pandit!A!gmail.com] Hi Sangeetha: Adding missing residues before simulation is an important task and people have their own preferences about the methodology. You could try the free program SWISS PDBViewer/DeepView program (Link 1) and follow the second link which explains the procedure with help of tutorials listed on the second link 1. http://spdbv.vital-it.ch/index.html 2. http://spdbv.vital-it.ch/build.html Best, Deepa On Mon, May 11, 2009 at 12:49 PM, Sangeetha Vimal srdshigella!A!gmail.com wrote: > > Sent to CCL by: "Sangeetha =A0Vimal" [srdshigella]^[gmail.com] > Hello everyone, > > Can someone post the tools/methods available for building missing residue= s in the crystal structure. I need the complete structure =A0for carrying o= ut simulation studies. > > thanks > sangeetha. > > > > -=3D This is automatically added to each message by the mailing script = =3D-> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml> =A0 =A0 =A0http://www.ccl.net/spammers.txt> > > From owner-chemistry@ccl.net Mon May 11 18:01:01 2009 From: "david marlan davma7[-]gmail.com" To: CCL Subject: CCL:G: Global geometry optimization Message-Id: <-39287-090511151703-31290-T3PLN94Q/QmemnKyJ1g0Xg.:.server.ccl.net> X-Original-From: david marlan Content-Type: multipart/alternative; boundary=001636499f5b7e6e200469a786c3 Date: Mon, 11 May 2009 23:25:43 +0430 MIME-Version: 1.0 Sent to CCL by: david marlan [davma7 . gmail.com] --001636499f5b7e6e200469a786c3 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Thanks for fast reply! Could you advice me this kind of software (MM) for quick coarse search of local minima. I know about Hyperchem in my opinion it works slow. As count of local minima rises exponentially with system size could you advice me such kind of software which can be used on high-perfomance computers, supercomputer (preferably using MPI parallelization). Thanks a lot! On Mon, May 11, 2009 at 6:34 PM, Alessandro Contini alessandro.contini() unimi.it wrote: > > Sent to CCL by: Alessandro Contini [alessandro.contini||unimi.it] > Hi, > doing a global optimization by mean of quantum mechanic methods might be > very time consuming. Probably it could be better performing a > conformational search by molecular mechanics and then perform geometry > optimization of all conformers within a certain energy treshold by mean > of a quantum chemistry method. > > Regards, > > Alessandro Contini > > > > Il giorno lun, 11/05/2009 alle 05.55 -0400, David Marlanov > davma7-,-gmail.com ha scritto: > > Sent to CCL by: "David Marlanov" [davma7]|[gmail.com] > > Dear colleagues! > > I'm not professional in quantum chemistry. > > I did local optimization in g03 and gamess (us) many times. As I > understood global geometry optimization (finding the geometry with global > energy minimum) was not implemented in these programs ( I mean Monte Carl= o > methods, genetic algorithm, etc.). Is there any program in quantum chemis= try > that can do such kind of optimization? > > I browsed the net and found many articles about this topic but not > implemented algorithm. > > > > Thanks a lot!> > > > -- > Dr. Alessandro Contini > DISMAB - Sezione di Chimica Organica "Alessandro Marchesini" > Universit=E0 degli Studi di Milano > Via Venezian, 21 20133 Milano > Tel. +390250314480 Fax. +390250314476 > e-mail alessandro.contini..unimi.it > skype alessandrocontini > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --001636499f5b7e6e200469a786c3 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Thanks for fast reply!
Could you advice me this kind of software (MM) fo= r quick coarse search of local
minima. I know=A0 about Hyperchem in my o= pinion it works slow.=A0
As=A0 count of local minima rises exponentiall= y=A0 with system size
could you advice me such kind of software which can be used on high-perfoma= nce computers, supercomputer
(preferably using MPI parallelization).
=
Thanks a lot!

On Mon, May 11, 2009 at= 6:34 PM, Alessandro Contini alessandro.contini() unimi.it <owner-chemistry . ccl.net> wrote:

Sent to CCL by: Alessandro Contini [alessandro.contini||unimi.it]
Hi,
doing a global optimization by mean of quantum mechanic methods might be very time consuming. Probably it could be better performing a
conformational search by molecular mechanics and then perform geometry
optimization of all conformers within a certain energy treshold by mean
of a quantum chemistry method.

Regards,

Alessandro Contini



Il giorno lun, 11/05/2009 alle 05.55 -0400, David Marlanov
davma7-,-gmail.com ha sc= ritto:
> Sent to CCL by: "David =A0Marlanov" [davma= 7]|[gmail.com]
> Dear colleagues!
> I'm not professional in quantum chemistry.
> I did local optimization =A0in g03 and gamess (us) many times. As I un= derstood global geometry optimization (finding the geometry with global ene= rgy minimum) was not implemented in these programs ( I mean Monte Carlo met= hods, genetic algorithm, etc.). Is there any program in quantum chemistry t= hat can do such kind of =A0optimization?
> I browsed the net and found many articles about this topic but not imp= lemented algorithm.
>
> Thanks a lot!>
>
--
Dr. Alessandro Contini
DISMAB - Sezione di Chimica Organica "Alessandro Marchesini"
Universit=E0 degli Studi di Milano
Via Venezian, 21 20133 Milano
Tel. +390250314480 Fax. +390250314476
e-mail alessandro.contini..un= imi.it
skype alessandrocontini



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

--001636499f5b7e6e200469a786c3-- From owner-chemistry@ccl.net Mon May 11 18:41:01 2009 From: "mohamed aish mhmdaish~!~yahoo.com" To: CCL Subject: CCL: Fitted Coefficient for Ex and Ec Parts Only Message-Id: <-39288-090511165724-13697-XBT8h2NpYnYvnOzPtFlqxA(a)server.ccl.net> X-Original-From: mohamed aish Content-Type: multipart/alternative; boundary="0-1581417101-1242075431=:96110" Date: Mon, 11 May 2009 13:57:11 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: mohamed aish [mhmdaish,,yahoo.com] --0-1581417101-1242075431=:96110 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hi Group;=0AMy question is about how the=0Acoefficients are calculated to c= orrect the exchange and correlation energies. I=0Aknow that the coefficient= s based on fitting to the one of the Thermochemical=0Adata; i.e. heats of f= ormation, atomization energy, electron affinity, proton=0Aaffinity and so o= n, and we know that the total energy, for example, for DFT is:=0AE(total) = =3D ENN + ENE + EKE + EJ + Ex + Ec=0AWhere; ENN: nuclear=0Anuclear repulsio= n=0AENE: nuclear electron =0AEKE: kinetic energy=0AEJ: electron-electron=0A= repulsion=0AEx: exchange energy=0AEc: correlation energy=0ANow my question = is: how the=0Afitted coefficients are calculated for Ex and Ec parts=0Aonly= without ENN, ENE, EKE and EJ?=0AIn other words: are the fitted coefficient= s for the Ex and Ec calculated alone?=0A =0AThanx=0A=0A=0A=0A --0-1581417101-1242075431=:96110 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
=0A=0A

Hi Group;

=0A=0A

My question is about how the=0Acoefficients are cal= culated to correct the exchange and correlation energies. I=0Aknow that the= coefficients based on fitting to the one of the Thermochemical=0Adata; i.e= . heats of formation, atomization energy, electron affinity, proton=0Aaffin= ity and so on, and we know that the total energy, for example, for DFT is:<= /p>=0A=0A

E(total) =3D ENN=0A+ ENE + EKE + EJ= + Ex + Ec

=0A=0A

Where; ENN: nuclear=0Anuclear repulsion=

=0A=0A

ENE: nuclear electron

=0A=0A

EKE: kinetic energy

=0A=0A

EJ: electron-electron=0Arepulsion

=0A= =0A

Ex: excha= nge energy

=0A=0A

Ec: correlation energy

=0A=0A

Now my question is: how the=0Afitted coefficients are calc= ulated for Ex and Ec parts=0Aonly without ENN, ENE, EKE and EJ?=0AIn other words: ar= e the fitted coefficients for the Ex and Ec=0Acalcula= ted alone?

=0A=0A

=A0

=0A=0A

Th= anx

=0A=0A=0A=0A=0A


=0A=0A --0-1581417101-1242075431=:96110-- From owner-chemistry@ccl.net Mon May 11 19:10:00 2009 From: "Zsolt Bikadi zsolt.bikadi*_*virtuadrug.com" To: CCL Subject: CCL: How to add missing residues Message-Id: <-39289-090511183708-29786-mqr/KkTbtrh5iMS8c48klg*o*server.ccl.net> X-Original-From: "Zsolt Bikadi" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Date: Tue, 12 May 2009 00:36:52 +0200 MIME-Version: 1.0 Sent to CCL by: "Zsolt Bikadi" [zsolt.bikadi-x-virtuadrug.com] Hello, I do not think that a viewer program is a good choice to add missing residues to a protein. It is a loop modelling task, which can be done by homology modeling softwares, try Rosetta commons or Modeller, both are free for academics. Sincerely, Zsolt Bikadi, PhD DockingServer Team ----- Original Message ----- > From: "Deepangi Pandit deepangi.pandita/gmail.com" To: "Bikadi, Zsolt " Sent: Monday, May 11, 2009 20:38 PM Subject: CCL: How to add missing residues Sent to CCL by: Deepangi Pandit [deepangi.pandit!A!gmail.com] Hi Sangeetha: Adding missing residues before simulation is an important task and people have their own preferences about the methodology. You could try the free program SWISS PDBViewer/DeepView program (Link 1) and follow the second link which explains the procedure with help of tutorials listed on the second link 1. http://spdbv.vital-it.ch/index.html 2. http://spdbv.vital-it.ch/build.html Best, Deepa On Mon, May 11, 2009 at 12:49 PM, Sangeetha Vimal srdshigella!A!gmail.com wrote: > > Sent to CCL by: "Sangeetha Vimal" [srdshigella]^[gmail.com] > Hello everyone, > > Can someone post the tools/methods available for building missing residues > in the crystal structure. I need the complete structure for carrying out > simulation studies. > > thanks > sangeetha.> > > -=his is automatically added to each message by the mailing script =http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Mon May 11 19:55:01 2009 From: "Herbert Fruchtl herbert.fruchtl**st-andrews.ac.uk" To: CCL Subject: CCL: Software suggestion Message-Id: <-39290-090511174617-22389-rJ6uWjhxiWd+5G17dcRIog[A]server.ccl.net> X-Original-From: Herbert Fruchtl Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 11 May 2009 22:45:27 +0100 MIME-Version: 1.0 Sent to CCL by: Herbert Fruchtl [herbert.fruchtl-*-st-andrews.ac.uk] For molecules, there are more builders (or programs that contain a builder) than you can shake a stick at: Molden, ECCE, Maestro (free for academics), Arguslab, to name a few free ones. For periodic systems, it's not so rosy. I generally use gdis (http://gdis.sourceforge.net/). I wouldn't use it to build a complicated structure from scratch, but you can add atoms by a mouseclick and drag them around on the screen, create a supercell, cleave a surface by specifying the Miller indices, etc. More powerful, but with a steep learning curve (which I haven't yet found the energy to master) due to the lack of a GUI is tetr (http://www.cmmp.ucl.ac.uk/~lev/codes/lev00/). A commercial product I haven't used, and don't know the price of, is Crystalmaker (http://www.crystalmaker.com/). You are right about Materials Studio. It's the best, but their "academic pricing" is based on the wrong meaning of "academic" :-). What doesn't improve things is that each of them supports a few file formats, but it's always the wrong ones, and Babel isn't that good at periodic structures either (no VASP, no SIESTA, no CASTEP). HTH, Herbert Quoting "Ugur Mart ugurmart ~~ yahoo.com" : > Can anyone suggest, if available, preferably free software for drawing > atomistic models, molecules and building crystal structures and surfaces. > Material Studio is I know one of the best but too expensive, isn't it? > Best regards > Ugur > > > > -- Herbert Fruchtl EaStCHEM Fellow School of Chemistry University of St Andrews ------------------------------------------------------------------ University of St Andrews Webmail: https://webmail.st-andrews.ac.uk