From owner-chemistry@ccl.net Wed Feb 17 05:01:02 2010 From: "Ramya iyer rinuiyer . gmail.com" To: CCL Subject: CCL: formulas Message-Id: <-41266-100217044514-24058-blNRsIHn8SsQsCkCYRU5bw||server.ccl.net> X-Original-From: "Ramya iyer" Date: Wed, 17 Feb 2010 04:45:09 -0500 Sent to CCL by: "Ramya iyer" [rinuiyer^_^gmail.com] Respected users, can anyone send me the formulas that are used to calculate the dipole moment, polarisability, frequency calculations force constants using guassian03 with sincerity Ramya From owner-chemistry@ccl.net Wed Feb 17 07:24:00 2010 From: "Dr. Attila Bende bende..itim-cj.ro" To: CCL Subject: CCL: Software for molecular cluster Message-Id: <-41267-100217072155-791-IHVngzbU4JVZXOCmxO0efg+/-server.ccl.net> X-Original-From: "Dr. Attila Bende" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Wed, 17 Feb 2010 15:46:23 +0200 (EET) MIME-Version: 1.0 Sent to CCL by: "Dr. Attila Bende" [bende.:.itim-cj.ro] Dear CCL Subscribers! Can anybody suggesting me a free molecular modeling software which is enable to generate a randomly distributed two-component (e.g. water and dimethylethyleneurea) molecular bulk. I would like to use for a molecular dynamics simulation. Many thanks. Attila -- Dr. Bende Attila (PhD) Senior Researcher II *************************************************** Molecular and Biomolecular Physics Department National Institute for R&D of Isotopic and Molecular Technologies Str. Donath nr.65-103, C.P.700 Cluj-Napoca, R-400293, Romania Phone:+40-264-584037, ext 194, Fax: +40-264-420042 e-mail: bende#%#itim-cj.ro, attlbende#%#gmail.com Web: http://www.itim-cj.ro/~bende http://www.researcherid.com/rid/A-6539-2008 *************************************************** From owner-chemistry@ccl.net Wed Feb 17 08:46:01 2010 From: "Hyungjun Kim hyungjun96*kaist.ac.kr" To: CCL Subject: CCL: Gaussian 09 PCM calculation output Message-Id: <-41268-100217071656-16582-w7Lxykb5uol4jCtYpVzWsQ],[server.ccl.net> X-Original-From: "Hyungjun Kim" Date: Wed, 17 Feb 2010 07:16:52 -0500 Sent to CCL by: "Hyungjun Kim" [hyungjun96:kaist.ac.kr] Dear CCL users, I used G09 program to calculate the solvation energy of metal complexes. There are, however, some problems. The calculation is done, but there are no PCM results. Here is my input. Do you have any idea? Basis sets and ECP are omitted. ************ %chk=01.B3LYP.solv.water.chk %mem=10GB %nproc=4 #P B3LYP/gen gfinput pseudo=read SP SCRF=(pcm,Solvent=Water) Solvation energy in water -4 1 26 0.000000 0.000000 0.000000 6 0.000000 0.000000 2.035581 7 0.000000 0.000000 3.218785 6 0.000000 2.035581 0.000000 7 0.000000 3.218785 0.000000 6 0.000000 -2.035581 0.000000 7 0.000000 -3.218785 0.000000 6 2.035581 0.000000 0.000000 7 3.218785 0.000000 0.000000 6 0.000000 0.000000 -2.035581 7 0.000000 0.000000 -3.218785 6 -2.035581 0.000000 0.000000 7 -3.218785 0.000000 0.000000 From owner-chemistry@ccl.net Wed Feb 17 09:21:02 2010 From: "Esteban Gabriel Vega Hissi egvega^gmail.com" To: CCL Subject: CCL: Software for molecular cluster Message-Id: <-41269-100217091031-16521-PiUtB0nmu9GwcB6mPcZufw---server.ccl.net> X-Original-From: Esteban Gabriel Vega Hissi Content-Type: multipart/alternative; boundary=0016e6d7eaa7fbeb01047fcc68f4 Date: Wed, 17 Feb 2010 11:09:58 -0300 MIME-Version: 1.0 Sent to CCL by: Esteban Gabriel Vega Hissi [egvega**gmail.com] --0016e6d7eaa7fbeb01047fcc68f4 Content-Type: text/plain; charset=ISO-8859-1 Hi, try PackMol http://www.ime.unicamp.br/~martinez/packmol/ Hope this help Esteban 2010/2/17 Dr. Attila Bende bende..itim-cj.ro > > Sent to CCL by: "Dr. Attila Bende" [bende.:.itim-cj.ro] > Dear CCL Subscribers! > > Can anybody suggesting me a free molecular modeling software which is > enable to generate a randomly distributed two-component (e.g. water and > dimethylethyleneurea) molecular bulk. I would like to use for a molecular > dynamics simulation. > > Many thanks. > Attila > > -- > Dr. Bende Attila (PhD) > Senior Researcher II > > *************************************************** > Molecular and Biomolecular Physics Department > National Institute for R&D of Isotopic and Molecular Technologies > Str. Donath nr.65-103, C.P.700 > Cluj-Napoca, R-400293, Romania > Phone:+40-264-584037, ext 194, Fax: +40-264-420042 > e-mail: bende]~[itim-cj.ro, attlbende]~[gmail.com > Web: http://www.itim-cj.ro/~bende > http://www.researcherid.com/rid/A-6539-2008 > ***************************************************> > > --0016e6d7eaa7fbeb01047fcc68f4 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi,
try PackMol
http://www.ime.unicamp.br/~martinez/packmol/

Hope this help=

Esteban

2010/2/17 Dr. Attila Bend= e bende..itim-cj.ro <= ;owner-chemistry:-:ccl.net>=

Sent to CCL by: "Dr. Attila Bende" [bende.:.itim-cj.ro]
Dear CCL Subscribers!

Can anybody suggesting me a free molecular modeling software which is
enable to generate a randomly distributed two-component (e.g. water and
dimethylethyleneurea) molecular bulk. I would like to use for a molecular dynamics simulation.

Many thanks.
Attila

--
Dr. Bende Attila (PhD)
Senior Researcher II

***************************************************
Molecular and Biomolecular Physics Department
National Institute for R&D of Isotopic and Molecular Technologies
Str. Donath nr.65-103, C.P.700
Cluj-Napoca, R-400293, Romania
Phone:+40-264-584037, ext 194, Fax: +40-264-420042
e-mail: bende]~[itim-cj.ro<= /a>, attlbende]~[gmail.com
Web: http://ww= w.itim-cj.ro/~bende
=A0 =A0 http://www.researcherid.com/rid/A-6539-2008
***************************************************



-=3D This is automatically added to each message by the mailing script =3D-=
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--0016e6d7eaa7fbeb01047fcc68f4-- From owner-chemistry@ccl.net Wed Feb 17 09:56:00 2010 From: "Andrew R Turner andrew.turner#%#ed.ac.uk" To: CCL Subject: CCL: Software for molecular cluster Message-Id: <-41270-100217090513-14164-TETc0Zhl+ZDJeYPTyxbngw###server.ccl.net> X-Original-From: Andrew R Turner Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Wed, 17 Feb 2010 13:31:09 +0000 MIME-Version: 1.0 Sent to CCL by: Andrew R Turner [andrew.turner_-_ed.ac.uk] Hi Attila, I have had success using 'Packmol': http://www.ime.unicamp.br/~martinez/packmol/ for this sort of task. Cheers Andy Quoting "Dr. Attila Bende bende..itim-cj.ro" : > > Sent to CCL by: "Dr. Attila Bende" [bende.:.itim-cj.ro] > Dear CCL Subscribers! > > Can anybody suggesting me a free molecular modeling software which is > enable to generate a randomly distributed two-component (e.g. water and > dimethylethyleneurea) molecular bulk. I would like to use for a molecular > dynamics simulation. > > Many thanks. > Attila > > -- > Dr. Bende Attila (PhD) > Senior Researcher II > > *************************************************** > Molecular and Biomolecular Physics Department > National Institute for R&D of Isotopic and Molecular Technologies > Str. Donath nr.65-103, C.P.700 > Cluj-Napoca, R-400293, Romania > Phone:+40-264-584037, ext 194, Fax: +40-264-420042 > e-mail: bende]~[itim-cj.ro, attlbende]~[gmail.com > Web: http://www.itim-cj.ro/~bende > http://www.researcherid.com/rid/A-6539-2008 > *************************************************** > > > > -=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=3D=3D=3D=3D=3D Dr Andrew R. Turner e: andrew.turner-,-ed.ac.uk t: +44 (0)131 651 3578 p: Edinburgh Parallel Computing Centre University of Edinburgh EH9 3JZ =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=3D=3D=3D=3D --=20 The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From owner-chemistry@ccl.net Wed Feb 17 10:31:00 2010 From: "Herbert Fruchtl herbert.fruchtl---st-andrews.ac.uk" To: CCL Subject: CCL: Software for molecular cluster Message-Id: <-41271-100217092820-29406-9ABQuv/af3w5XdvU09IQjw~!~server.ccl.net> X-Original-From: Herbert Fruchtl Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 17 Feb 2010 13:46:53 +0000 MIME-Version: 1.0 Sent to CCL by: Herbert Fruchtl [herbert.fruchtl]![st-andrews.ac.uk] I have not used this, but the description sounds like what you are looking for: http://www.ime.unicamp.br/~martinez/packmol/ The bigger MD programs (AMBER, CHARMM, etc.) should also come with tools to do this. HTH, Herbert Dr. Attila Bende bende..itim-cj.ro wrote: > Sent to CCL by: "Dr. Attila Bende" [bende.:.itim-cj.ro] > Dear CCL Subscribers! > > Can anybody suggesting me a free molecular modeling software which is > enable to generate a randomly distributed two-component (e.g. water and > dimethylethyleneurea) molecular bulk. I would like to use for a molecular > dynamics simulation. > > Many thanks. > Attila > -- Herbert Fruchtl Senior Scientific Computing Officer School of Chemistry, School of Mathematics and Statistics University of St Andrews -- The University of St Andrews is a charity registered in Scotland: No SC013532 From owner-chemistry@ccl.net Wed Feb 17 11:06:01 2010 From: "Mannan k malie_03^^^yahoo.co.in" To: CCL Subject: CCL: how to define protein flexibilty Message-Id: <-41272-100217100355-26178-aaDUj9UZEfjEkzLElTdzkQ|a|server.ccl.net> X-Original-From: "Mannan k" Date: Wed, 17 Feb 2010 10:03:51 -0500 Sent to CCL by: "Mannan k" [malie_03::yahoo.co.in] Two homologous proteins were studied using MD with an active compound reported for one of the protein. One of them distrupts the flexibilty, while other adapts to the compound invovled, How will you define this adaptability, is it induced fit? one of the protein, neither gave a compact fit for the compound nor releasing the compound (in other words neither releases nor interacts, but the compound still bound in the active site and making the active site much larger for the compound to interact) Mannan From owner-chemistry@ccl.net Wed Feb 17 11:40:00 2010 From: "Tristan Youngs t.youngs]![qub.ac.uk" To: CCL Subject: CCL: Software for molecular cluster Message-Id: <-41273-100217102021-10542-LiNnJljaR6JbBZf5SHWukg%server.ccl.net> X-Original-From: Tristan Youngs Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 17 Feb 2010 14:50:02 +0000 MIME-Version: 1.0 Sent to CCL by: Tristan Youngs [t.youngs|-|qub.ac.uk] You could try out Aten (www.projectaten.net) - sounds like it will do what you're after! Dr. Attila Bende bende..itim-cj.ro wrote: > Sent to CCL by: "Dr. Attila Bende" [bende.:.itim-cj.ro] > Dear CCL Subscribers! > > Can anybody suggesting me a free molecular modeling software which is > enable to generate a randomly distributed two-component (e.g. water and > dimethylethyleneurea) molecular bulk. I would like to use for a molecular > dynamics simulation. > > Many thanks. > Attila > > -- Dr. T. Youngs (t.youngs:_:qub.ac.uk) Atomistic Simulation Centre Old Physics Building Queen's University Belfast Belfast, BT7 1NN, N.I. From owner-chemistry@ccl.net Wed Feb 17 12:21:01 2010 From: "Esteban Gabriel Vega Hissi egvega^gmail.com" To: CCL Subject: CCL:G: Gaussian 09 PCM calculation output Message-Id: <-41274-100217103020-15010-tlvfyTwp/KULOfHT0EValw:server.ccl.net> X-Original-From: Esteban Gabriel Vega Hissi Content-Type: multipart/alternative; boundary=0016e6db2b1c78c849047fcd86df Date: Wed, 17 Feb 2010 12:29:47 -0300 MIME-Version: 1.0 Sent to CCL by: Esteban Gabriel Vega Hissi [egvega]-[gmail.com] --0016e6db2b1c78c849047fcd86df Content-Type: text/plain; charset=ISO-8859-1 Hi, It's nothing wrong, just G09 works different from 03 for SCRF calculation. http://www.gaussian.com/g_tech/g_ur/k_scrf.htm Esteban 2010/2/17 Hyungjun Kim hyungjun96*kaist.ac.kr > > Sent to CCL by: "Hyungjun Kim" [hyungjun96:kaist.ac.kr] > Dear CCL users, > > I used G09 program to calculate the solvation energy of metal complexes. > > There are, however, some problems. > > The calculation is done, but there are no PCM results. > > Here is my input. Do you have any idea? > > Basis sets and ECP are omitted. > > > ************ > %chk=01.B3LYP.solv.water.chk > %mem=10GB > %nproc=4 > #P B3LYP/gen gfinput pseudo=read SP SCRF=(pcm,Solvent=Water) > > Solvation energy in water > > -4 1 > 26 0.000000 0.000000 0.000000 > 6 0.000000 0.000000 2.035581 > 7 0.000000 0.000000 3.218785 > 6 0.000000 2.035581 0.000000 > 7 0.000000 3.218785 0.000000 > 6 0.000000 -2.035581 0.000000 > 7 0.000000 -3.218785 0.000000 > 6 2.035581 0.000000 0.000000 > 7 3.218785 0.000000 0.000000 > 6 0.000000 0.000000 -2.035581 > 7 0.000000 0.000000 -3.218785 > 6 -2.035581 0.000000 0.000000 > 7 -3.218785 0.000000 0.000000> > > --0016e6db2b1c78c849047fcd86df Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi,

It's nothing wrong, just G09 works different from 03 for SC= RF calculation.

http://www.gaussian.com/g_tech/g_ur/k_scrf.htm

Esteban

2010/2/17 Hyungjun Kim hyungjun96*kaist.ac.kr <owner-chemistry::ccl.net>

Sent to CCL by: "Hyungjun =A0Kim" [hyungjun96:kaist.ac.kr]
Dear CCL users,

=A0I used G09 program to calculate the solvation energy of metal complexes.=

=A0There are, however, some problems.

=A0The calculation is done, but there are no PCM results.

=A0Here is my input. Do you have any idea?

=A0Basis sets and ECP are omitted.


************
%chk=3D01.B3LYP.solv.water.chk
%mem=3D10GB
%nproc=3D4
#P B3LYP/gen gfinput pseudo=3Dread SP SCRF=3D(pcm,Solvent=3DWater)

Solvation energy in water

-4 1
=A026 0.000000 0.000000 0.000000
=A06 0.000000 0.000000 2.035581
=A07 0.000000 0.000000 3.218785
=A06 0.000000 2.035581 0.000000
=A07 0.000000 3.218785 0.000000
=A06 0.000000 -2.035581 0.000000
=A07 0.000000 -3.218785 0.000000
=A06 2.035581 0.000000 0.000000
=A07 3.218785 0.000000 0.000000
=A06 0.000000 0.000000 -2.035581
=A07 0.000000 0.000000 -3.218785
=A06 -2.035581 0.000000 0.000000
=A07 -3.218785 0.000000 0.000000



-=3D This is automatically added to each message by the mailing script =3D-=
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--0016e6db2b1c78c849047fcd86df-- From owner-chemistry@ccl.net Wed Feb 17 12:50:00 2010 From: "=?iso-8859-1?Q?Gonzalo_Jim=E9nez-Os=E9s?= gonzalo.jimenez:unirioja.es" To: CCL Subject: CCL:G: Gaussian 09 PCM calculation output Message-Id: <-41275-100217105028-1946-z9mzxn4dAfHNW0X8wq0aRA__server.ccl.net> X-Original-From: =?iso-8859-1?Q?Gonzalo_Jim=E9nez-Os=E9s?= Content-Transfer-Encoding: 8bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Date: Wed, 17 Feb 2010 15:57:57 +0100 MIME-Version: 1.0 Sent to CCL by: =?iso-8859-1?Q?Gonzalo_Jim=E9nez-Os=E9s?= [gonzalo.jimenez#,#unirioja.es] Dear Hyungjun, Have you tried to read the keywords section of the G09 users's manual? Some changes have been made in the PCM subroutines and one usually should read the manual (at least the part one wants to use) BEFORE submitting jobs and asking the CCL when the first (trivial) problem arise. Otherwise, and in the case that reading the manual was too painful and boring, one should ask the Gaussian help service because you have paid for it (supossedly). It should be remembered that the CCL is not the Gaussian (nor any other specific software) user's list or help service. Others are paid for doing that job. As an exception, I'm going to give you an answer, only to illustrate what happens when one spend just a couple of minutes searching and reading. Your question is clearly addressed in the SCRF section of the manual (you can go directly to the end): ****** PCM Energy. In general, energy output from the default SCRF method appears in the normal way within the output file. For example, here are the sections of the output file containing the predicted energy from a Hartree-Fock and > from an MP2 PCM calculation: Hartree-Fock SCRF calculation: SCF Done: E(RHF) = -99.4687828290 A.U. after 8 cycles Convg = 0.2586D-08 -V/T = 2.0015 MP2 SCRF calculation: E2 = -0.1192799427D+00 EUMP2 = -0.99584491345297D+02 The predicted energy in solution includes all computed corrections (unlike in Gaussian 03 output). ****** I honestly think that it simply takes less time to search in the manual (it's also freely available online) that writing an email to the whole community. My two cents, Gonzalo -------------------------------------------------- > From: "Hyungjun Kim hyungjun96*kaist.ac.kr" Sent: Wednesday, February 17, 2010 1:16 PM To: "Osés,GonzaloJiménez" Subject: CCL: Gaussian 09 PCM calculation output > > Sent to CCL by: "Hyungjun Kim" [hyungjun96:kaist.ac.kr] > Dear CCL users, > > I used G09 program to calculate the solvation energy of metal complexes. > > There are, however, some problems. > > The calculation is done, but there are no PCM results. > > Here is my input. Do you have any idea? > > Basis sets and ECP are omitted. > > > ************ > %chk=01.B3LYP.solv.water.chk > %mem=10GB > %nproc=4 > #P B3LYP/gen gfinput pseudo=read SP SCRF=(pcm,Solvent=Water) > > Solvation energy in water > > -4 1 > 26 0.000000 0.000000 0.000000 > 6 0.000000 0.000000 2.035581 > 7 0.000000 0.000000 3.218785 > 6 0.000000 2.035581 0.000000 > 7 0.000000 3.218785 0.000000 > 6 0.000000 -2.035581 0.000000 > 7 0.000000 -3.218785 0.000000 > 6 2.035581 0.000000 0.000000 > 7 3.218785 0.000000 0.000000 > 6 0.000000 0.000000 -2.035581 > 7 0.000000 0.000000 -3.218785 > 6 -2.035581 0.000000 0.000000 > 7 -3.218785 0.000000 0.000000> > From owner-chemistry@ccl.net Wed Feb 17 13:26:01 2010 From: "srikanth peddireddy srikanth.pedireddy~~gmail.com" To: CCL Subject: CCL: formulas Message-Id: <-41276-100217110807-19566-VCjg7WvqRuSdtEA8cdS1Bw!A!server.ccl.net> X-Original-From: srikanth peddireddy Content-Type: multipart/alternative; boundary=000e0cd1153e5e9f7f047fcd2528 Date: Wed, 17 Feb 2010 16:02:58 +0100 MIME-Version: 1.0 Sent to CCL by: srikanth peddireddy [srikanth.pedireddy(a)gmail.com] --000e0cd1153e5e9f7f047fcd2528 Content-Type: text/plain; charset=ISO-8859-1 I didn't get you wat u exactly need formulae or keywords. # b3lyp/6-31g* fopt freq this is at DFT level of theory and the basis set is " 6-31g* " " FOPT " keyword is for full optimization and "FREQ" keyword is for Frequency calculations. by default it calculates dipolemoment and Polarizibilities which you can get > from output file. On Wed, Feb 17, 2010 at 10:45 AM, Ramya iyer rinuiyer . gmail.com < owner-chemistry(0)ccl.net> wrote: > > Sent to CCL by: "Ramya iyer" [rinuiyer^_^gmail.com] > Respected users, > can anyone send me the formulas that are used to calculate the > dipole moment, polarisability, frequency calculations force constants using > guassian03 > > > > with sincerity > Ramya> > > --000e0cd1153e5e9f7f047fcd2528 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable I didn't get you wat u exactly need formulae or keywords.=A0

# = b3lyp/6-31g* fopt freq

this is at DFT level of theory and the basis= set is "=A0 6-31g* "

" FOPT " keyword is for f= ull optimization and "FREQ" keyword is for Frequency calculations= .

by default it calculates dipolemoment and Polarizibilities which you ca= n get from output file.

On Wed, Feb 17, 2= 010 at 10:45 AM, Ramya iyer rinuiyer . gmail.c= om <own= er-chemistry(0)ccl.net> wrote:

Sent to CCL by: "Ramya =A0iyer" [rinuiyer^_^gmail.com]
Respected users,
=A0 =A0 =A0 =A0 =A0 =A0can anyone send me the formulas that are used to ca= lculate the dipole moment, polarisability, frequency calculations force con= stants using guassian03



with sincerity
Ramya



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--000e0cd1153e5e9f7f047fcd2528-- From owner-chemistry@ccl.net Wed Feb 17 14:10:01 2010 From: "Siegfried Hoefinger siegfried.hoefinger * unibo.it" To: CCL Subject: CCL:G: POLCH 2.3 now supporting biomembranes Message-Id: <-41277-100217122558-21404-Ms/PdcpmMXkvKWOQtTzA7g^server.ccl.net> X-Original-From: "Siegfried Hoefinger" Date: Wed, 17 Feb 2010 12:25:54 -0500 Sent to CCL by: "Siegfried Hoefinger" [siegfried.hoefinger:_:unibo.it] Greetings, POLCH 2.3 www-service available at --> http://84.113.253.84/~polch New features include, *) Support for biomembranous environments *) GPU acceleration *) Temperature dependence for solvent water >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> As previously, POLCH is an implicit solvation program for proteins (# residues < 500). It is based on the Poisson-Boltzmann approach and has the following characteristics, a) Consideration of electrostatic as well as non-polar contributions b) PCM-like decomposition into properly separated individual contributions c) Usage of Gaussian cube format for ESP maps (electrostatic potentials) for straightforward visualization with VMD or MOLDEN d) Availability of several solvents/environments, ie water, methanol, ethanol, n-octanol, cyclohexane and a biomembrane-mimic best sig -- Siegfried Hoefinger Dipartimento di Chimica "G. Ciamician" Universita di Bologna Via F. Selmi, 2 40126 Bologna, ITALY Tel: +39 051 209 / 9578 Fax: +39 051 209 / 9456 http://members.chello.at/siegfried.hoefinger/home_page/sh.html From owner-chemistry@ccl.net Wed Feb 17 14:47:01 2010 From: "Vinod kasam vinod.kasam_-_uky.edu" To: CCL Subject: CCL: Redocking with Fred docking tool Message-Id: <-41278-100217135856-8819-w1Mf3llePDy3lQovPh2Q+A]=[server.ccl.net> X-Original-From: "Vinod kasam" Date: Wed, 17 Feb 2010 13:58:51 -0500 Sent to CCL by: "Vinod kasam" [vinod.kasam^^uky.edu] Dear all I am a new user of Fred docking tool. Can somebody please tell me the syntax to perform redocking with Fred. I want to see the RMSD against a set of PDBs. I using Fred 2.2.5 version. Thanks in advance, From owner-chemistry@ccl.net Wed Feb 17 18:10:00 2010 From: "James Gary Prudhomme jprudhomme]-[healthtech.com" To: CCL Subject: CCL: CHI's 10th Structure-Based Design Conference Message-Id: <-41279-100217161226-24823-LJgLj/7dwXr1ZdmbYo8ROw:+:server.ccl.net> X-Original-From: "James Gary Prudhomme" Date: Wed, 17 Feb 2010 16:12:22 -0500 Sent to CCL by: "James Gary Prudhomme" [jprudhomme:_:healthtech.com] Join us for CHI's 10th Anniversary Event... STRUCTURE-BASED DRUG DESIGN: Multidisciplinary Innovations and Structural Insights to Enhance Drug Discovery June 23-25, 2010 Royal Sonesta Hotel, Cambridge, MA Register by March 26 and Save up to $350 www.healthtech.com/sbd In this program, we wish to highlight some recent breakthrough stories and successes using SBDD driven by medicinal chemistry, computational and biophysical approaches. This conference continues to offer both new attendees and alumni insights into the latest work of community thought-leaders as well as invaluable networking opportunities. Topics Include: - Selectivity Optimization: Using Structure to Optimize Selectivity - In Silico Discovery of Small Molecule Binders - New Computational Methods in SBDD - Targeting of Protein-Protein Interactions - New Advances in Docking - Impact of SBDD on Small Molecule Drug Discovery - GPCR Drug Discovery - Workshop: Therapeutic Target Space: Methods for Druggability Assessment View the full agenda and register at www.healthtech.com/SBD or call 781-972-5400 Interested in Sponsoring and/or Exhibiting? Contact Katelin Fitzgerald at 781-972-5458, kfitzgerald\a/healthtech.com Organizer: Cambridge Healthtech Institute