From owner-chemistry@ccl.net Thu Nov 11 00:52:00 2010 From: "Sayan Mondal sayanmondal.ncbs%a%gmail.com" To: CCL Subject: CCL:G: Thermochemistry calculations Message-Id: <-43136-101111005052-7995-zhVDxiQdsVfV4ii5VEe1zA],[server.ccl.net> X-Original-From: Sayan Mondal Content-Type: multipart/alternative; boundary=001485f85afa16d5d00494c08e55 Date: Thu, 11 Nov 2010 11:20:45 +0530 MIME-Version: 1.0 Sent to CCL by: Sayan Mondal [sayanmondal.ncbs%x%gmail.com] --001485f85afa16d5d00494c08e55 Content-Type: text/plain; charset=ISO-8859-1 Hi Hamdy, For detailed description of computing deltaG, deltaH and deltaS from a gaussian frequency job, take a look to the gaussian official document : "Thermochemistry in Gaussian" at http://www.gaussian.com/g_whitepap/thermo.htm sayan On Thu, Nov 11, 2010 at 3:16 AM, Hamdy El Sheshtawy h.elsheshtawy a jacobs-university.de wrote: > > Sent to CCL by: Hamdy El Sheshtawy [h.elsheshtawy]![jacobs-university.de] > Dear all, > I am doing solvent effect calculations with B3LYP/6-311G** on radicals and > I want to know how to extract the Delta G and DH and DS solvations > >> from the frequency output. >> > > For eample in the output file I have these informations: > > Zero-point correction= 0.288623 > (Hartree/Particle) > Thermal correction to Energy= 0.303786 > Thermal correction to Enthalpy= 0.304731 > Thermal correction to Gibbs Free Energy= 0.243475 > Sum of electronic and zero-point Energies= -657.083380 > Sum of electronic and thermal Energies= -657.068216 > Sum of electronic and thermal Enthalpies= -657.067272 > Sum of electronic and thermal Free Energies= -657.128527 > > E (Thermal) CV S > KCal/Mol Cal/Mol-Kelvin Cal/Mol-Kelvin > Total 190.629 57.627 128.923 > Electronic 0.000 0.000 1.377 > Translational 0.889 2.981 41.889 > Rotational 0.889 2.981 32.465 > Vibrational 188.851 51.665 53.191 > > > best > Hamdyhttp://www.ccl.net/chemistry/sub_unsub.shtml> > Job: http://www.ccl.net/jobsConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > -- Sayan Mondal Graduate Student Dr. Mrinalini Puranik's Lab National Centre for Biological Sciences, TIFR Bangalore - 560065 INDIA Ph: +91-080-2366 6161 Fax: +91-080-2363 6662 --001485f85afa16d5d00494c08e55 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Hamdy,

For detailed description of computing deltaG, deltaH and d= eltaS from a gaussian frequency job, take a look to the gaussian official d= ocument :
"Thermochemistry in Gaussian" at=A0 http://= www.gaussian.com/g_whitepap/thermo.htm

sayan

On Thu, Nov 11, 2010 at 3:16 AM= , Hamdy El Sheshtawy h.elsheshtawy a jacobs-university.de <owner-chemistry^-^ccl.net> wrote:

Sent to CCL by: Hamdy El Sheshtawy [h.elsheshtawy]![jacobs-university.de]
Dear all,
I am doing solvent effect calculations with B3LYP/6-311G** on radicals and = I want to know how to extract the Delta G and DH and DS solvations
> from the frequency output.

For eample in the output file I have these informations:

=A0Zero-point correction=3D =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0= =A0 0.288623 (Hartree/Particle)
=A0Thermal correction to Energy=3D =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00= .303786
=A0Thermal correction to Enthalpy=3D =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00.3= 04731
=A0Thermal correction to Gibbs Free Energy=3D =A0 =A0 =A0 =A0 0.243475
=A0Sum of electronic and zero-point Energies=3D =A0 =A0 =A0 =A0 =A0 -657.08= 3380
=A0Sum of electronic and thermal Energies=3D =A0 =A0 =A0 =A0 =A0 =A0 =A0-65= 7.068216
=A0Sum of electronic and thermal Enthalpies=3D =A0 =A0 =A0 =A0 =A0 =A0-657.= 067272
=A0Sum of electronic and thermal Free Energies=3D =A0 =A0 =A0 =A0 -657.1285= 27

=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 E (Thermal) =A0 =A0 =A0 =A0 =A0 = =A0 CV =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0S
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0KCal/Mol =A0 =A0 =A0 =A0Cal/Mol= -Kelvin =A0 =A0Cal/Mol-Kelvin
=A0Total =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0190.629 =A0 =A0 =A0 =A0 =A0 =A0= 57.627 =A0 =A0 =A0 =A0 =A0 =A0128.923
=A0Electronic =A0 =A0 =A0 =A0 =A0 =A0 =A0 0.000 =A0 =A0 =A0 =A0 =A0 =A0 =A0= 0.000 =A0 =A0 =A0 =A0 =A0 =A0 =A01.377
=A0Translational =A0 =A0 =A0 =A0 =A0 =A00.889 =A0 =A0 =A0 =A0 =A0 =A0 =A02.= 981 =A0 =A0 =A0 =A0 =A0 =A0 41.889
=A0Rotational =A0 =A0 =A0 =A0 =A0 =A0 =A0 0.889 =A0 =A0 =A0 =A0 =A0 =A0 =A0= 2.981 =A0 =A0 =A0 =A0 =A0 =A0 32.465
=A0Vibrational =A0 =A0 =A0 =A0 =A0 =A0188.851 =A0 =A0 =A0 =A0 =A0 =A0 51.66= 5 =A0 =A0 =A0 =A0 =A0 =A0 53.191


best
Hamdy



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--
Sayan Mondal
Graduat= e Student
Dr. Mrinalini Puranik's Lab
National Centre for Biologi= cal Sciences, TIFR
Bangalore - 560065
INDIA
Ph:=A0 +91-080-2366 61= 61
Fax: +91-080-2363 6662

--001485f85afa16d5d00494c08e55-- From owner-chemistry@ccl.net Thu Nov 11 08:44:01 2010 From: "baljinder grewal baljinder7]^[gmail.com" To: CCL Subject: CCL:G: HOMA analysis Message-Id: <-43137-101110231549-27856-WRm2YYiWJMwmphgBQh3pkQ],[server.ccl.net> X-Original-From: "baljinder grewal" Date: Wed, 10 Nov 2010 23:15:40 -0500 Sent to CCL by: "baljinder grewal" [baljinder7%a%gmail.com] Dear all, I need to quantify the extent of -electron delocalization of series of compound.In literature it is reported to be done by HOMA (harmonic oscillator measure of aromaticity) analysis using gaussian software , but method to do same is not reported .Kindly suggest any keyword or specific tutorial i have to refer . Thanks in advance From owner-chemistry@ccl.net Thu Nov 11 09:18:00 2010 From: "Toomas Tamm tt-ccl2||yki.ttu.ee" To: CCL Subject: CCL: G95 compiler issue Message-Id: <-43138-101111090429-32167-RpW1TXXOhVhPF5hZTHDWGg^_^server.ccl.net> X-Original-From: Toomas Tamm Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Thu, 11 Nov 2010 16:03:21 +0200 Mime-Version: 1.0 Sent to CCL by: Toomas Tamm [tt-ccl2],[yki.ttu.ee] Hello John, > Sent to CCL by: John McKelvey [jmmckel^^^gmail.com] > I am trying to compile a code which the second routine is called with > an argument such as 'second(integer)'.. At *compile* timeG95 > complains that this is not standard.. Unlike C and many other languages, where you can redefine, eg sin(x) to return whatever value you please, Fortran has the notion of intrinsic functions: sin(x) always returns the sine of the argument and the compiler with complain if you try to provide your own implementation of function sin(x). Thus the question comes down to whether second(i) is defined as intrinsic in Fortran 95 standard. If it is, your program violates the standard and a different name for the function should be chosen. If it is not, there may be other solutions, up to filing a bug report against the compiler. -- Toomas Tamm e-mail: tt-ccl2 (at) kky . ttu . ee Chair of Inorganic Chemistry voice: INT+372-620-2810 Tallinn University of Technology fax: INT+372-620-2828 Ehitajate tee 5, EE-19086 Tallinn, Estonia http://www.kk.ttu.ee/toomas/ From owner-chemistry@ccl.net Thu Nov 11 10:22:00 2010 From: "neeraj misra neerajmisra^hotmail.com" To: CCL Subject: CCL: Structure and property Message-Id: <-43139-101111101848-24499-eHfa3kw6oqYy1fFTFAObag/a\server.ccl.net> X-Original-From: "neeraj misra" Date: Thu, 11 Nov 2010 10:18:47 -0500 Sent to CCL by: "neeraj misra" [neerajmisra]=[hotmail.com] DEAR CCLER'S I AM WORKING ON TWO ANALOGUES OF A BIOMOLECULE, AND I WONDER HOW TO RELATE/CALCULATE THE STRUCTURAL PROPERTIES(USING DFT) WITH ITS BIOACTIVITY.CAN THE BIOACTIVITY BE RELATED/INTERPRETED IN TERMS OF RESULTS OBTAINED BY QUANTUM CHEMICAL CALCULATIONS(DFT).ANY SUGGESTION IN THIS REGARD WOULD BE GREATLY APPRECIATED. REGARDS NEERAJ From owner-chemistry@ccl.net Thu Nov 11 11:10:00 2010 From: "Antonio Chana achana _ iqfr.csic.es" To: CCL Subject: CCL: Structure and property Message-Id: <-43140-101111110754-19680-zgnCPK5oXeBrT8x/ROY91w .. server.ccl.net> X-Original-From: Antonio Chana Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 11 Nov 2010 17:05:53 +0100 MIME-Version: 1.0 Sent to CCL by: Antonio Chana [achana ~ iqfr.csic.es] Dear Neeraj, that's actually the underlying idea of any SAR or -getting quantitative- QSAR study. Basically you must calculate any property you can think of (in your case usingDFT, although why being so close minded?), and checking wether there are any correlation between the properties you obtained and the bioactivity. So the answer is yes, you can do it. Inet is plenty of information about such approaches. Regards, Antonio El 11/11/2010 16:18, neeraj misra neerajmisra^hotmail.com escribió: > Sent to CCL by: "neeraj misra" [neerajmisra]=[hotmail.com] > DEAR CCLER'S > I AM WORKING ON TWO ANALOGUES OF A BIOMOLECULE, AND I WONDER HOW TO RELATE/CALCULATE THE STRUCTURAL PROPERTIES(USING DFT) WITH ITS BIOACTIVITY.CAN THE BIOACTIVITY BE RELATED/INTERPRETED IN TERMS OF RESULTS OBTAINED BY QUANTUM CHEMICAL CALCULATIONS(DFT).ANY SUGGESTION IN THIS REGARD WOULD BE GREATLY APPRECIATED. > > REGARDS > NEERAJ> > > From owner-chemistry@ccl.net Thu Nov 11 11:44:00 2010 From: "John McKelvey jmmckel(!)gmail.com" To: CCL Subject: CCL: G95 compiler issue Message-Id: <-43141-101111112923-28720-l5oLo9itXFejfOI0sVxG8w~~server.ccl.net> X-Original-From: John McKelvey Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 11 Nov 2010 11:29:14 -0500 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel,+,gmail.com] Toomas, Good point! John On Thu, Nov 11, 2010 at 9:03 AM, Toomas Tamm tt-ccl2||yki.ttu.ee wrote: > > Sent to CCL by: Toomas Tamm [tt-ccl2],[yki.ttu.ee] > Hello John, > >> Sent to CCL by: John McKelvey [jmmckel^^^gmail.com] > >> I am trying to compile a code which the second routine is called with >> an argument such as 'second(integer)'..  At *compile* timeG95 >> complains that this is not standard.. > > Unlike C and many other languages, where you can redefine, eg sin(x) to > return whatever value you please, Fortran has the notion of intrinsic > functions: sin(x) always returns the sine of the argument and the > compiler with complain if you try to provide your own implementation of > function sin(x). > > Thus the question comes down to whether second(i) is defined as > intrinsic in Fortran 95 standard. If it is, your program violates the > standard and a different name for the function should be chosen. If it > is not, there may be other solutions, up to filing a bug report against > the compiler. > > -- > Toomas Tamm                                 e-mail: tt-ccl2 (at) kky . ttu . ee > Chair of Inorganic Chemistry                voice:  INT+372-620-2810 > Tallinn University of Technology            fax:    INT+372-620-2828 > Ehitajate tee 5, EE-19086 Tallinn, Estonia  http://www.kk.ttu.ee/toomas/>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > > -- John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel=-=gmail.com From owner-chemistry@ccl.net Thu Nov 11 12:20:00 2010 From: "Eduard Matito ematito!=!gmail.com" To: CCL Subject: CCL:G: HOMA analysis Message-Id: <-43142-101111100552-15576-3m8AiSjCiSy584UCtvCixg^^server.ccl.net> X-Original-From: Eduard Matito Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Thu, 11 Nov 2010 16:05:39 +0100 Mime-Version: 1.0 (Apple Message framework v936) Sent to CCL by: Eduard Matito [ematito%a%gmail.com] I'm afraid HOMA it's not implemented in Gaussian, but its calculation can be done on the back of an envelope, you only need distances and few constants. This topic was already discussed in CCL. See e.g.: http://www.ccl.net/cgi-bin/ccl/message-new?2009+05+11+010 Eduard On Nov 11, 2010, at 5:15 AM, baljinder grewal baljinder7]^[gmail.com wrote: > > Sent to CCL by: "baljinder grewal" [baljinder7%a%gmail.com] > Dear all, > I need to quantify the extent of -electron delocalization of series > of compound.In literature it is reported to be done by HOMA > (harmonic oscillator measure of aromaticity) analysis using gaussian > software , but method to do same is not reported .Kindly suggest any > keyword or specific tutorial i have to refer . > > Thanks in advance > > > > -= 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) Phone: +48914441436 http://ematito.webs.com From owner-chemistry@ccl.net Thu Nov 11 12:55:00 2010 From: "Vishal Kohli vishal.kohli:_:hotmail.com" To: CCL Subject: CCL: Reforming Dimer Message-Id: <-43143-101111101219-20051-pwHVnsQ1wdUfLvs+wm89Fg.@.server.ccl.net> X-Original-From: "Vishal Kohli" Date: Thu, 11 Nov 2010 10:12:17 -0500 Sent to CCL by: "Vishal Kohli" [vishal.kohli.%%.hotmail.com] Hi guys, I have a crystal structure of a molecule however it is only the monomer and was wondering if anyone knew of a program that would help me to reform the homodimer, thanks Vishal From owner-chemistry@ccl.net Thu Nov 11 13:59:00 2010 From: "Jamin Krinsky jamink{:}berkeley.edu" To: CCL Subject: CCL:G: Gaussian03 error: GetSCM: Allocation for FCRed failed: Message-Id: <-43144-101111135759-30713-y0D4BI40JjXGfxSJOgfOcA]-[server.ccl.net> X-Original-From: Jamin Krinsky Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 11 Nov 2010 10:57:50 -0800 MIME-Version: 1.0 Sent to CCL by: Jamin Krinsky [jamink++berkeley.edu] Dear Maciej, The keywords you are using specify the maximum amount of disk space, but the error message looks like you are out of memory. You should specify in the %mem section something a little less than the physical memory you have on your system. For example, if you are running on a computer (or cluster node) that has 8GB of RAM, you could specify something like %mem=7GB. If the job still fails it means that your system does not have enough installed memory to do the size of job you are trying, although a transition state search (assuming it's DFT?) should run fine any modern system. Hope this helps. Jamin On Wed, Nov 10, 2010 at 5:49 AM, Maciej Maslyk maciejmarcin.maslyk:ceu.es wrote: > > Sent to CCL by: "Maciej  Maslyk" [maciejmarcin.maslyk+/-ceu.es] > > > Hi, I got this error doing QST3 with G03. Even if I put MaxDisc=10GB or 100GB and %RWF=loc1,size1,loc2,size2, the problem still appears. Help, please! > > GetSCM: Allocation for FCRed failed: > Core=-2041361480 Need=241511221 GauSpace=2012942344 MaxMem=268435456 Avail=238352522. > Error termination via Lnk1e in /usr/local/g03/l716.exe at Tue Nov 2 17:16:45 2010. > Job cpu time: 0 days 5 hours 47 minutes 27.7 seconds. > File lengths (MBytes): RWF= 1793 Int= 0 D2E= 0 Chk= 154 Scr= 1>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > > From owner-chemistry@ccl.net Thu Nov 11 16:12:00 2010 From: "Soren Eustis soreneustis[-]gmail.com" To: CCL Subject: CCL: Reforming Dimer Message-Id: <-43145-101111154128-16883-n006ofG+K5qW+zu613JYww * server.ccl.net> X-Original-From: Soren Eustis Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Thu, 11 Nov 2010 21:41:53 +0100 Mime-Version: 1.0 (iPhone Mail 8A293) Sent to CCL by: Soren Eustis [soreneustis]*[gmail.com] The monomer you see is from a crystal, therefore the dimer would have to be the same geometry. A simple method would be to perform a simulated annealing with two frozen monomers. Of course, solid state structures may or may not be realistic for your analysis. Regards, Soren > From owner-chemistry@ccl.net Thu Nov 11 20:09:00 2010 From: "jacqueline cawthray jcawth01:+:gmail.com" To: CCL Subject: CCL:G: Reading fchk files in gv 3.0 Message-Id: <-43146-101111200815-14766-w7cKBpxAa3daA/RbQ5k0ow-.-server.ccl.net> X-Original-From: "jacqueline cawthray" Date: Thu, 11 Nov 2010 20:08:14 -0500 Sent to CCL by: "jacqueline cawthray" [jcawth01##gmail.com] Hi I have g09 optimization jobs run on a remote computer and want to view the results (particularly surfaces) using Gaussview 3.0 on Ubuntu on a local computer. I have tried reading the file.chk directly but get the error "can't find the formchk utility". It is there but I'm not sure how to go about this. I have also tried converting the file.chk to file.fchk using either g09 or g03. Using g03 generates an error writing the fchk file and using g09, gview won't open it. Thanks for your time. Regards JC From owner-chemistry@ccl.net Thu Nov 11 20:44:00 2010 From: "Close, David M. CLOSED a mail.etsu.edu" To: CCL Subject: CCL:G: Reading fchk files in gv 3.0 Message-Id: <-43147-101111203816-8825-E0jsM/jVCD+fGuMzwRm/9w _ server.ccl.net> X-Original-From: "Close, David M." Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 12 Nov 2010 01:37:58 +0000 MIME-Version: 1.0 Sent to CCL by: "Close, David M." [CLOSED]=[mail.etsu.edu] Jacqueline: This topic was discussed on the CCL just 1-2 months ago. I seem to recall that there were several solutions offered. One solution was to generate the .fchk file in the actual calculation by adding the keyword formcheck on the command line. Also someone mentioned that G03 may not be able to convert a check file generated by G09. So you could do a quick check at try to generate the 'fchk file on the remote computer, and then see if you can read it locally. Regards, Dave Close. -----Original Message----- > From: owner-chemistry+closed==etsu.edu*o*ccl.net [mailto:owner-chemistry+closed==etsu.edu*o*ccl.net] On Behalf Of jacqueline cawthray jcawth01:+:gmail.com Sent: Thursday, November 11, 2010 8:08 PM To: Close, David M. Subject: CCL:G: Reading fchk files in gv 3.0 Sent to CCL by: "jacqueline cawthray" [jcawth01##gmail.com] Hi I have g09 optimization jobs run on a remote computer and want to view the results (particularly surfaces) using Gaussview 3.0 on Ubuntu on a local computer. I have tried reading the file.chk directly but get the error "can't find the formchk utility". It is there but I'm not sure how to go about this. I have also tried converting the file.chk to file.fchk using either g09 or g03. Using g03 generates an error writing the fchk file and using g09, gview won't open it. Thanks for your time. Regards JChttp://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 Thu Nov 11 22:54:00 2010 From: "irfan ahmad irfaahmad.^_^.gmail.com" To: CCL Subject: CCL: Reforming Dimer Message-Id: <-43148-101111224608-28711-jESpMT0ZB3KDTh5oF+Kefw^_^server.ccl.net> X-Original-From: irfan ahmad Content-Type: multipart/alternative; boundary=0016368322e4ba104a0494d2ed2b Date: Thu, 11 Nov 2010 19:45:59 -0800 MIME-Version: 1.0 Sent to CCL by: irfan ahmad [irfaahmad ~ gmail.com] --0016368322e4ba104a0494d2ed2b Content-Type: text/plain; charset=ISO-8859-1 You can use Mercury software and open crystal structure there, then click the packing. You will get its packing, after that you can select dimer from the packing. Dr. IRFAN AHMAD On Thu, Nov 11, 2010 at 7:12 AM, Vishal Kohli vishal.kohli:_:hotmail.com < owner-chemistry,ccl.net> wrote: > > Sent to CCL by: "Vishal Kohli" [vishal.kohli.,.hotmail.com] > Hi guys, > I have a crystal structure of a molecule however it is only the monomer > and was wondering if anyone knew of a program that would help me to reform > the homodimer, > > > thanks > Vishal> > > -- --0016368322e4ba104a0494d2ed2b Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
You can use Mercury software and open crystal structure there, then cl= ick the packing. You will get its packing, after that you can select dimer = > from the packing.
Dr. IRFAN AHMAD
On Thu, Nov 11, 2010 at 7:12 AM, Vishal Kohli vi= shal.kohli:_:hotmail.com <owner-chemistry,ccl.net> wrote:

Sent to CCL by: "Vishal= =A0Kohli" [vishal.kohli.,.hotmail.com]
Hi guys,
I have a crystal structure of a molecule however it is only the= monomer =A0and was wondering if anyone knew of a program that would help m= e to reform the homodimer,


thanks
Vishal



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