From owner-chemistry@ccl.net Wed Jun 18 04:12:01 2008 From: "Antje Wolf antje.wolf(-)scai.fraunhofer.de" To: CCL Subject: CCL: rmsd calculation Message-Id: <-37171-080618041010-12438-XxWg+v3RceloXUtyP6Yk3g*server.ccl.net> X-Original-From: "Antje Wolf" Date: Wed, 18 Jun 2008 04:10:07 -0400 Sent to CCL by: "Antje Wolf" [antje.wolf]~[scai.fraunhofer.de] Hi, I am looking for a (free) tool for calculating the RMSD between two molecule conformations, preferably a script or command line tool as I want to use it in batch mode. It would be great if this tool also includes the possibility to do a clustering. Perhaps, someone has a good suggestion. Thanks in advance, Antje From owner-chemistry@ccl.net Wed Jun 18 06:03:00 2008 From: "Michel PETITJEAN michel.petitjean::cea.fr" To: CCL Subject: CCL: RE : rmsd calculation Message-Id: <-37172-080618055421-21882-n00+Rkv0puiljsa5u3KXIw^-^server.ccl.net> X-Original-From: "Michel PETITJEAN" Content-class: urn:content-classes:message Content-Type: multipart/mixed; boundary="----_=_NextPart_001_01C8D129.3F8A783C" Date: Wed, 18 Jun 2008 11:51:21 +0200 MIME-Version: 1.0 Sent to CCL by: "Michel PETITJEAN" [michel.petitjean{:}cea.fr] This is a multi-part message in MIME format. ------_=_NextPart_001_01C8D129.3F8A783C Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable The freeware ARMS does that (scriptable, unix): http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#ARMS Michel Petitjean, DSV/iBiTec-S/SB2SM (CNRS URA 2096), CEA Saclay, bat. 528, 91191 Gif-sur-Yvette Cedex, France. Phone: +331 6908 4006 / Fax: +331 6908 4007 E-mail: michel.petitjean()cea.fr http://petitjeanmichel.free.fr/itoweb.petitjean.shape.html -------- Message d'origine-------- De: Antje Wolf antje.wolf(-)scai.fraunhofer.de = [mailto:owner-chemistry()ccl.net] Date: mer. 18/06/2008 10:10 =C0: Michel PETITJEAN Objet : CCL: rmsd calculation =20 Sent to CCL by: "Antje Wolf" [antje.wolf]~[scai.fraunhofer.de] Hi, I am looking for a (free) tool for calculating the RMSD between two = molecule conformations, preferably a script or command line tool as I = want to use it in batch mode. It would be great if this tool also includes the possibility to do a = clustering. Perhaps, someone has a good suggestion. Thanks in advance, Antje ------_=_NextPart_001_01C8D129.3F8A783C-- From owner-chemistry@ccl.net Wed Jun 18 06:37:00 2008 From: "James Robinson James.Robinson*prosonix.co.uk" To: CCL Subject: CCL:G: failure to convergence at l502 Message-Id: <-37173-080618054629-19492-mT2SG0ARrEoTw3dafbMDGA:+:server.ccl.net> X-Original-From: "James Robinson" Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C8D128.0C8CF56F" Date: Wed, 18 Jun 2008 10:45:31 +0100 MIME-Version: 1.0 Sent to CCL by: "James Robinson" [James.Robinson|prosonix.co.uk] This is a multi-part message in MIME format. ------_=_NextPart_001_01C8D128.0C8CF56F Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable Do check the charge and multiplicity card in your calculation, O 4 means charge of zero and S=3D4, quartic spin state, you may need to make the calculation unrestricted. A ground state is normally charge=3D0 and = S=3D1 (all electrons paired).=20 =20 Dr James J Robinson Senior Scientist Prosonix Ltd Magdalen Centre Robert Robinson Avenue Oxford Science Park Oxford, Oxon. OX4 4GA, UK. +44(0) 1865 784243 http://www.prosonix.co.uk =20 =20 P Please consider the environment - do you really need to print this email? =20 Prosonix Limited registered office is One London Wall, London, EC2Y 5AB, United Kingdom. Registered in England and Wales, number 5679156. ************************************************************************ ******************** Any opinions expressed in this email are those of the individual and not necessarily the Company. This email and any files transmitted with it, including replies and forwarded copies (which may contain alterations) subsequently transmitted from the Company, are confidential and solely for the use of the intended recipient. If you are not the intended recipient or the person responsible for delivering to the intended recipient, be advised that you have received this email in error and that any use is strictly prohibited. ************************************************************************ ******************** =20 =20 ________________________________ > From: owner-chemistry,,ccl.net [mailto:owner-chemistry,,ccl.net]=20 Sent: 18 June 2008 01:51 To: James Robinson Subject: CCL:G: failure to convergence at l502 =20 =20 =20 best wishes Guanna Li gnli|-|dicp.ac.cn =20 =20 ________________________________ > From: gnli [mailto:gnli|-|dicp.ac.cn]=20 Sent: Tuesday, June 17, 2008 7:10 PM To: (owner-chemistry|-|ccl.net) Subject: CCL:G:failure to convergence at l502 =20 Dear CCLer, I help colleague to calculate a system that, organic small molecules chelate to Co using G03. We guess a structure initially. It always failure to convergence at L502. The input file attached as follow, please help me to find out the problem. Thank you very much!=20 =20 %mem=3D3000MB %nproc=3D4 #P opt freq hf/gen pseudo=3Dread geom=3Dconnectivity =20 Title Card Required =20 0 4 C 4.74525520 -3.67512720 1.64681896 O 5.10508314 -2.53544589 2.19217125 C 4.85956762 -5.18545529 1.73580983 C 4.58521757 -5.60919292 0.46470138 C 4.27249582 -4.36562042 -0.46416142 O 4.23298657 -4.30269998 -1.71604055 C 4.64216253 -7.09031581 0.12698424 C 4.97515467 -7.93564207 1.14761972 C 5.28119481 -7.36913787 2.57683373 N 4.05062182 -3.31713815 0.50165371 O 2.69433378 -3.21505697 0.57982506 H 4.43223021 -7.44969985 -0.86158082 H 5.02970811 -8.99089610 0.97112771 H 5.54497203 -8.04711255 3.36349801 H 2.34385831 -2.89349992 -0.25428833 C 5.31341686 1.66031382 -0.78512135 C 4.98786778 3.93187093 -1.40686954 C 6.56916759 1.77044156 -0.62648683 C 5.01015974 0.22804829 -0.43793402 C 6.51978706 4.14521452 -1.21018903 H 4.38053767 4.74962945 -1.71969890 C 7.10784955 0.39759476 -0.20243518 C 7.29384554 3.09703004 -0.83215327 O 3.91309793 -0.31812257 -0.16717367 N 6.15960375 -0.79342173 -0.34646311 H 6.95576183 5.10869234 -1.37357152 O 8.27856372 0.25784896 0.23375347 H 8.35076285 3.19374590 -0.68744872 O 7.00683015 -1.30547240 0.58396554 H 6.66521277 -1.12500116 1.46484117 N 4.43827012 2.76039479 -1.19014305 N 5.22156463 -6.08676647 2.83244035 Co 4.78541031 -1.70466342 0.53684476 =20 1 2 2.0 3 1.0 10 1.0 2 33 1.0 3 4 2.0 32 1.0 4 5 1.0 7 1.0 5 6 2.0 10 1.0 6 7 8 2.0 12 1.0 8 9 1.0 13 1.0 9 14 1.0 32 2.0 10 11 1.0 33 1.0 11 15 1.0 12 13 14 15 16 18 2.0 19 1.0 31 1.0 17 20 1.0 21 1.0 31 2.0 18 22 1.0 23 1.0 19 24 2.0 25 1.0 20 23 2.0 26 1.0 21 22 27 2.0 25 1.0 23 28 1.0 24 33 1.0 25 29 1.0 33 1.0 26 27 28 29 30 1.0 30 31 32 33 =20 C O N H 0 6-31g **** Co 0 LanL2DZ **** Co 0 LanL2DZ **** best wishes Guanna Li =20 =20 ------_=_NextPart_001_01C8D128.0C8CF56F Content-Type: text/html; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable

Do check the charge and = multiplicity card in your calculation, O 4 means charge of zero and S=3D4, quartic spin = state, you may need to make the calculation unrestricted. A ground state is = normally charge=3D0 and S=3D1 (all electrons paired). =

 

Dr James J = Robinson

Senior = Scientist

Prosonix = Ltd

Magdalen = Centre

Robert Robinson = Avenue

Oxford Science = Park

Oxford, Oxon.

OX4 4GA, = UK.

+44(0) 1865 = 784243

http://www.prosonix.co.uk

 

=

P Please consider the environment - = do you really need to print this email?

 

=

Prosonix Limited registered office is One = London Wall, London, = EC2Y 5AB, United Kingdom. Registered in = England and Wales, number = 5679156.

******************************************= **************************************************
Any opinions expressed in this email are those of the individual and not necessarily the Company. This email and any files transmitted with it, including replies and forwarded copies (which may contain alterations) subsequently transmitted from the Company, are confidential and solely = for the use of the intended recipient. If you are not the intended recipient or = the person responsible for delivering to the intended recipient, be advised = that you have received this email in error and that any use is strictly = prohibited.

*************************************************************************= *******************

 

=

 

=

From: owner-chemistry,,ccl.net [mailto:owner-chemistry,,ccl.net]
Sent: 18 June 2008 = 01:51
To: James Robinson
Subject: CCL:G: failure = to convergence at l502

 

 <= /span>

 <= /span>

best wishes
Guanna Li
gnli|-|dicp.ac.cn<= /span>

 

From: gnli [mailto:gnli|-|dicp.ac.cn]
Sent: Tuesday, June 17, = 2008 7:10 PM
To: = (owner-chemistry|-|ccl.net)
Subject: CCL:G:failure to convergence at l502

 

Dear = CCLer,

I help colleague to = calculate a system that, organic small molecules chelate to Co using G03. We guess a structure initially. It always failure to convergence at L502. The input = file attached as follow, please help me to find out the = problem.

Thank you very much! =

 

%mem=3D3000MB

%nproc=3D4<= /font>

#P opt freq hf/gen = pseudo=3Dread geom=3Dconnectivity

 

Title Card = Required

 

0 = 4

 C   &nbs= p;            = ;  4.74525520   -3.67512720    = 1.64681896

 O   &nbs= p;            = ;  5.10508314   -2.53544589    = 2.19217125

 C       &nb= sp;          4.85956762   -5.18545529    = 1.73580983

 C   &nbs= p;            = ;  4.58521757   -5.60919292    = 0.46470138

 C   &nbs= p;            = ;  4.27249582   -4.36562042   = -0.46416142

 O   &nbs= p;            = ;  4.23298657   -4.30269998   = -1.71604055

 C   &nbs= p;            = ;  4.64216253   -7.09031581    = 0.12698424

 C   &nbs= p;            = ;  4.97515467   -7.93564207    = 1.14761972

 C   &nbs= p;            = ;  5.28119481   -7.36913787    = 2.57683373

 N   &nbs= p;            = ;  4.05062182   -3.31713815    = 0.50165371

 O   &nbs= p;            = ;  2.69433378   -3.21505697    = 0.57982506

 H   &nbs= p;            = ;  4.43223021   -7.44969985   = -0.86158082

 H       &nb= sp;          5.02970811   -8.99089610    = 0.97112771

 H   &nbs= p;            = ;  5.54497203   -8.04711255    = 3.36349801

 H   &nbs= p;            = ;  2.34385831   -2.89349992   = -0.25428833

 C   &nbs= p;            = ;  5.31341686    1.66031382   = -0.78512135

 C   &nbs= p;            = ;  4.98786778    3.93187093   = -1.40686954

 C   &nbs= p;            = ;  6.56916759    1.77044156   = -0.62648683

 C   &nbs= p;            = ;  5.01015974    0.22804829   = -0.43793402

 C   &nbs= p;            = ;  6.51978706    4.14521452   = -1.21018903

 H   &nbs= p;            = ;  4.38053767    4.74962945   = -1.71969890

 C   &nbs= p;            = ;  7.10784955    0.39759476   = -0.20243518

 C       &nb= sp;          7.29384554    3.09703004   = -0.83215327

 O   &nbs= p;            = ;  3.91309793   -0.31812257   = -0.16717367

 N   &nbs= p;            = ;  6.15960375   -0.79342173   = -0.34646311

 H   &nbs= p;            = ;  6.95576183    5.10869234   = -1.37357152

 O   &nbs= p;            = ;  8.27856372    0.25784896    = 0.23375347

 H   &nbs= p;            = ;  8.35076285    3.19374590   = -0.68744872

 O   &nbs= p;            = ;  7.00683015   -1.30547240    = 0.58396554

 H   &nbs= p;            = ;  6.66521277   -1.12500116    = 1.46484117

 N   &nbs= p;            = ;  4.43827012    2.76039479   = -1.19014305

 N   &nbs= p;            = ;  5.22156463   -6.08676647    = 2.83244035

 Co    &nb= sp;            4.78541031   -1.70466342    = 0.53684476

 

 1 2 2.0 3 1.0 10 = 1.0

 2 33 = 1.0

 3 4 2.0 32 = 1.0

 4 5 1.0 7 = 1.0

 5 6 2.0 10 = 1.0

 6

 7 8 2.0 12 = 1.0

 8 9 1.0 13 = 1.0

 9 14 1.0 32 = 2.0

 10 11 1.0 33 = 1.0

 11 15 = 1.0

 12

 13

 14

 15

 16 18 2.0 19 1.0 31 = 1.0

 17 20 1.0 21 1.0 31 = 2.0

 18 22 1.0 23 = 1.0

 19 24 2.0 25 = 1.0

 20 23 2.0 26 = 1.0

 21

 22 27 2.0 25 = 1.0

 23 28 = 1.0

 24 33 = 1.0

 25 29 1.0 33 = 1.0

 26

 27

 28

 29 30 = 1.0

 30

 31

 32

 33

 

C O N H = 0

6-31g

****=

Co = 0

LanL2DZ

****=

Co = 0

LanL2DZ

****=

best wishes
Guanna Li

 

 

------_=_NextPart_001_01C8D128.0C8CF56F-- From owner-chemistry@ccl.net Wed Jun 18 07:12:00 2008 From: "Alcides Simao alsimao{=}gmail.com" To: CCL Subject: CCL: PESscan Message-Id: <-37174-080618062512-4504-1TX1ljP7QbCSnUe4f9MR0w+*+server.ccl.net> X-Original-From: "Alcides Simao" Content-Type: multipart/alternative; boundary="----=_Part_1419_15909262.1213784700604" Date: Wed, 18 Jun 2008 11:25:00 +0100 MIME-Version: 1.0 Sent to CCL by: "Alcides Simao" [alsimao[-]gmail.com] ------=_Part_1419_15909262.1213784700604 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hello All! Dear Alexandra, Yes, you can do PES of uni, bi, tri, 'all-that-your-cpu-can-hold-as-long-as-it-doesn't-bust' dimensions ;) Just be careful with the parameters you use to make the relaxed PES. Peter mencioned also the use of the opt=loose for when some optimizations get stuck. It's a way of working, although I use a different approach. I reoptimize points that don't converge in a solo calculation, with the same converge criteria, for a longer time. IMHO, I get a tidier PES scan! Nevertheless, I will not dare to say that Peter way of working isn't correct - I just don't use it. Loose criteria means a less demanding convergence tolerance. But I'll try to use his way just to compare with mine, and see what I get. Best Regards, Alcides ------=_Part_1419_15909262.1213784700604 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hello All!

Dear Alexandra,

Yes, you can do PES of uni, bi, tri, 'all-that-your-cpu-can-hold-as-long-as-it-doesn't-bust' dimensions ;)

Just be careful with the parameters you use to make the relaxed PES.

Peter mencioned also the use of the opt=loose for when some optimizations get stuck. It's a way of working, although I use a different approach. I reoptimize points that don't converge in a solo calculation, with the same converge criteria, for a longer time. IMHO, I get a tidier PES scan! Nevertheless, I will not dare to say that Peter way of working isn't correct - I just don't use it. Loose criteria means a less demanding convergence tolerance. But I'll try to use his way just to compare with mine, and see what I get.

Best Regards,

Alcides
------=_Part_1419_15909262.1213784700604-- From owner-chemistry@ccl.net Wed Jun 18 07:50:01 2008 From: "John McKelvey jmmckel ~ gmail.com" To: CCL Subject: CCL:G: failure to convergence at l502 Message-Id: <-37175-080618074712-15598-qwC6cT1GXHL44L9zY69Sig##server.ccl.net> X-Original-From: "John McKelvey" Content-Type: multipart/alternative; boundary="----=_Part_9863_6235024.1213789611806" Date: Wed, 18 Jun 2008 07:46:51 -0400 MIME-Version: 1.0 Sent to CCL by: "John McKelvey" [jmmckel(_)gmail.com] ------=_Part_9863_6235024.1213789611806 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hello! This is an oblique approach to the problem in case that the guessed geometry might not be adequate: Optimize the structure using a semi-empirical method such as MOPAC2007/PM6 [free to academics]. The resulting geometry will likely be quite decent for starting ab initio or DFT codes. Cheers, John McKelvey On Tue, Jun 17, 2008 at 8:51 PM, gnli gnli^dicp.ac.cn < owner-chemistry|,|ccl.net> wrote: > * * > > * * > > best wishes > Guanna Li > gnli|-|dicp.ac.cn > > > > ------------------------------ > > *From:* gnli [mailto:gnli|-|dicp.ac.cn] > *Sent:* Tuesday, June 17, 2008 7:10 PM > *To:* (owner-chemistry|-|ccl.net) > *Subject:* CCL:G:failure to convergence at l502 > > > > *Dear CCLer,* > > *I help colleague to calculate a system that, organic small molecules > chelate to Co using G03. We guess a structure initially. It always failure > to convergence at L502. The input file attached as follow, please help me to > find out the problem.* > > *Thank you very much! * > > * * > > *%mem=3000MB* > > *%nproc=4* > > *#P opt freq hf/gen pseudo=read geom=connectivity* > > * * > > *Title Card Required* > > * * > > *0 4* > > * C 4.74525520 -3.67512720 1.64681896* > > * O 5.10508314 -2.53544589 2.19217125* > > * **C 4.85956762 -5.18545529 1.73580983* > > * C 4.58521757 -5.60919292 0.46470138* > > * C 4.27249582 -4.36562042 -0.46416142* > > * O 4.23298657 -4.30269998 -1.71604055* > > * C 4.64216253 -7.09031581 0.12698424* > > * C 4.97515467 -7.93564207 1.14761972* > > * C 5.28119481 -7.36913787 2.57683373* > > * N 4.05062182 -3.31713815 0.50165371* > > * O 2.69433378 -3.21505697 0.57982506* > > * H 4.43223021 -7.44969985 -0.86158082* > > * **H 5.02970811 -8.99089610 0.97112771* > > * H 5.54497203 -8.04711255 3.36349801* > > * H 2.34385831 -2.89349992 -0.25428833* > > * C 5.31341686 1.66031382 -0.78512135* > > * C 4.98786778 3.93187093 -1.40686954* > > * C 6.56916759 1.77044156 -0.62648683* > > * C 5.01015974 0.22804829 -0.43793402* > > * C 6.51978706 4.14521452 -1.21018903* > > * H 4.38053767 4.74962945 -1.71969890* > > * C 7.10784955 0.39759476 -0.20243518* > > * **C 7.29384554 3.09703004 -0.83215327* > > * O 3.91309793 -0.31812257 -0.16717367* > > * N 6.15960375 -0.79342173 -0.34646311* > > * H 6.95576183 5.10869234 -1.37357152* > > * O 8.27856372 0.25784896 0.23375347* > > * H 8.35076285 3.19374590 -0.68744872* > > * O 7.00683015 -1.30547240 0.58396554* > > * H 6.66521277 -1.12500116 1.46484117* > > * N 4.43827012 2.76039479 -1.19014305* > > * N 5.22156463 -6.08676647 2.83244035* > > * Co 4.78541031 -1.70466342 0.53684476* > > * * > > * 1 2 2.0 3 1.0 10 1.0* > > * 2 33 1.0* > > * 3 4 2.0 32 1.0* > > * 4 5 1.0 7 1.0* > > * 5 6 2.0 10 1.0* > > * 6* > > * 7 8 2.0 12 1.0* > > * 8 9 1.0 13 1.0* > > * 9 14 1.0 32 2.0* > > * 10 11 1.0 33 1.0* > > * 11 15 1.0* > > * 12* > > * 13* > > * 14* > > * 15* > > * 16 18 2.0 19 1.0 31 1.0* > > * 17 20 1.0 21 1.0 31 2.0* > > * 18 22 1.0 23 1.0* > > * 19 24 2.0 25 1.0* > > * 20 23 2.0 26 1.0* > > * 21* > > * 22 27 2.0 25 1.0* > > * 23 28 1.0* > > * 24 33 1.0* > > * 25 29 1.0 33 1.0* > > * 26* > > * 27* > > * 28* > > * 29 30 1.0* > > * 30* > > * 31* > > * 32* > > * 33* > > * * > > *C O N H 0* > > *6-31g* > > ****** > > *Co 0* > > *LanL2DZ* > > ****** > > *Co 0* > > *LanL2DZ* > > ****** > > best wishes > Guanna Li > > > > > ------=_Part_9863_6235024.1213789611806 Content-Type: text/html; charset=ISO-2022-JP Content-Transfer-Encoding: 7bit Content-Disposition: inline Hello!

This is an oblique approach to the problem in case that the guessed geometry might not be adequate:  Optimize the structure using a semi-empirical method such as MOPAC2007/PM6 [free to academics].  The resulting geometry will likely be quite decent for starting ab initio or DFT codes.

Cheers,

John McKelvey

On Tue, Jun 17, 2008 at 8:51 PM, gnli gnli^dicp.ac.cn <owner-chemistry|,|ccl.net> wrote:

 

 

best wishes
Guanna Li
gnli|-|dicp.ac.cn



From: gnli [mailto:gnli|-|dicp.ac.cn]
Sent: Tuesday, June 17, 2008 7:10 PM
To: (owner-chemistry|-|ccl.net)
Subject: CCL:G:failure to convergence at l502

 

Dear CCLer,

I help colleague to calculate a system that, organic small molecules chelate to Co using G03. We guess a structure initially. It always failure to convergence at L502. The input file attached as follow, please help me to find out the problem.

Thank you very much!

 

%mem=3000MB

%nproc=4

#P opt freq hf/gen pseudo=read geom=connectivity

 

Title Card Required

 

0 4

 C                  4.74525520   -3.67512720    1.64681896

 O                  5.10508314   -2.53544589    2.19217125

 C                  4.85956762   -5.18545529    1.73580983

 C                  4.58521757   -5.60919292    0.46470138

 C                  4.27249582   -4.36562042   -0.46416142

 O                  4.23298657   -4.30269998   -1.71604055

 C                  4.64216253   -7.09031581    0.12698424

 C                  4.97515467   -7.93564207    1.14761972

 C                  5.28119481   -7.36913787    2.57683373

 N                  4.05062182   -3.31713815    0.50165371

 O                  2.69433378   -3.21505697    0.57982506

 H                  4.43223021   -7.44969985   -0.86158082

 H                  5.02970811   -8.99089610    0.97112771

 H                  5.54497203   -8.04711255    3.36349801

 H                  2.34385831   -2.89349992   -0.25428833

 C                  5.31341686    1.66031382   -0.78512135

 C                  4.98786778    3.93187093   -1.40686954

 C                  6.56916759    1.77044156   -0.62648683

 C                  5.01015974    0.22804829   -0.43793402

 C                  6.51978706    4.14521452   -1.21018903

 H                  4.38053767    4.74962945   -1.71969890

 C                  7.10784955    0.39759476   -0.20243518

 C                  7.29384554    3.09703004   -0.83215327

 O                  3.91309793   -0.31812257   -0.16717367

 N                  6.15960375   -0.79342173   -0.34646311

 H                  6.95576183    5.10869234   -1.37357152

 O                  8.27856372    0.25784896    0.23375347

 H                  8.35076285    3.19374590   -0.68744872

 O                  7.00683015   -1.30547240    0.58396554

 H                  6.66521277   -1.12500116    1.46484117

 N                  4.43827012    2.76039479   -1.19014305

 N                  5.22156463   -6.08676647    2.83244035

 Co                 4.78541031   -1.70466342    0.53684476

 

 1 2 2.0 3 1.0 10 1.0

 2 33 1.0

 3 4 2.0 32 1.0

 4 5 1.0 7 1.0

 5 6 2.0 10 1.0

 6

 7 8 2.0 12 1.0

 8 9 1.0 13 1.0

 9 14 1.0 32 2.0

 10 11 1.0 33 1.0

 11 15 1.0

 12

 13

 14

 15

 16 18 2.0 19 1.0 31 1.0

 17 20 1.0 21 1.0 31 2.0

 18 22 1.0 23 1.0

 19 24 2.0 25 1.0

 20 23 2.0 26 1.0

 21

 22 27 2.0 25 1.0

 23 28 1.0

 24 33 1.0

 25 29 1.0 33 1.0

 26

 27

 28

 29 30 1.0

 30

 31

 32

 33

 

C O N H 0

6-31g

****

Co 0

LanL2DZ

****

Co 0

LanL2DZ

****

best wishes
Guanna Li

 

 


------=_Part_9863_6235024.1213789611806-- From owner-chemistry@ccl.net Wed Jun 18 08:33:00 2008 From: "Arthur computationalboy ~~ gmail.com" To: CCL Subject: CCL: Ploting protein-protein interactions Message-Id: <-37176-080618072323-31263-VHboCs/mhQEb1YM7a1hs/Q**server.ccl.net> X-Original-From: "Arthur" Content-Type: multipart/alternative; boundary="----=_NextPart_08061818111089021503012_002" Date: Wed, 18 Jun 2008 18:11:13 +0800 MIME-Version: 1.0 Sent to CCL by: "Arthur"[computationalboy[a]gmail.com] ------=_NextPart_08061818111089021503012_002 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: base64 RGVhciBhbGw6DQpOb3cgSSBhbSBkZXZvdGVkIGludG8gY29tcHV0YXRpb25hbCByZXNlYXJjaCBv biBwcm90ZWluLXByb3RlaW4gaW50ZXJhY3Rpb25zLiBJIGhhdmUgZ290IHRoZSBwcm90ZWluLXBy b3RlaW4gY29tcGxleCBzdHJ1Y3R1cmUsIGFuZCB3YW50IHRvIGZpbmQgc29tZSBpbnRlcmFjdGlv bnMgYmV0d2VlbiB0aGVtLCBzdWNoIGFzIGh5ZHJvZ2VuLWJvbmRpbmcsIGh5ZHJvcGhvYmljLCBl dGMuDQpDb3VsZCBhbnkgb25lIHJlY29tbWVuZCBhbnkgc29mdHdhcmUgZm9yIHZpc3VhbGl6ZSBz dWNoIGludGVyYWN0aW9ucz8gU29tZSBzb2Z0d2FyZSBzdWNoIGFzIGxpZ3Bsb3QgaXMgdXNlZnVs IGZvciBwbG90dGluZyBwcm90ZWluLWxpZ2FuZCBpbnRlcmFjdGlvbiBvdGhlciB0aGFuIG1hY3Jv IGludGVyYWN0aW9ucy4NClRoYW5rcyBpbiBhZHZhbmNlIQ0KWW91cnMgQXJ0aHVyDQo= ------=_NextPart_08061818111089021503012_002 Content-Type: text/html; charset="GB2312" Content-Transfer-Encoding: base64 PEhUTUw+PEhFQUQ+DQo8TUVUQSBjb250ZW50PSJLc0RIVE1MRURMaWIub2N4LCBGcmVlV2FyZSBI VE1MIEVkaXRvciAxLjE2NC4yLCA/S3VydCBTZW5mZXIiIA0KbmFtZT1HRU5FUkFUT1I+DQo8TUVU QSBodHRwLWVxdWl2PUNvbnRlbnQtVHlwZSBjb250ZW50PSJ0ZXh0L2h0bWw7IGNoYXJzZXQ9R0Iy MzEyIj48L0hFQUQ+DQo8Qk9EWT4NCjxQPkRlYXIgYWxsOjwvUD4NCjxQPk5vdyBJIGFtIGRldm90 ZWQgaW50byBjb21wdXRhdGlvbmFsIHJlc2VhcmNoIG9uIHByb3RlaW4tcHJvdGVpbiBpbnRlcmFj dGlvbnMuIA0KSSBoYXZlIGdvdCB0aGUgcHJvdGVpbi1wcm90ZWluIGNvbXBsZXggc3RydWN0dXJl LCBhbmQgd2FudCB0byBmaW5kIHNvbWUgDQppbnRlcmFjdGlvbnMgYmV0d2VlbiB0aGVtLCBzdWNo IGFzIGh5ZHJvZ2VuLWJvbmRpbmcsIGh5ZHJvcGhvYmljLCBldGMuPC9QPg0KPFA+Q291bGQgYW55 IG9uZSByZWNvbW1lbmQmbmJzcDthbnkgc29mdHdhcmUgZm9yJm5ic3A7dmlzdWFsaXplIHN1Y2gg DQppbnRlcmFjdGlvbnM/Jm5ic3A7U29tZSBzb2Z0d2FyZSBzdWNoIGFzIGxpZ3Bsb3QgaXMgdXNl ZnVsIGZvciBwbG90dGluZyANCnByb3RlaW4tbGlnYW5kIGludGVyYWN0aW9uIG90aGVyIHRoYW4g bWFjcm8gaW50ZXJhY3Rpb25zLjwvUD4NCjxQPlRoYW5rcyBpbiBhZHZhbmNlITwvUD4NCjxQPllv dXJzIEFydGh1cjwvUD4NCjxQPiZuYnNwOzwvUD48L0JPRFk+PC9IVE1MPg0K ------=_NextPart_08061818111089021503012_002-- From owner-chemistry@ccl.net Wed Jun 18 09:07:01 2008 From: "Alberto Sergio Garay sgaray_._fbcb.unl.edu.ar" To: CCL Subject: CCL: Problems with some Tinker's routines.......... Message-Id: <-37177-080618075201-19541-SP8qyzEMwm+dd7GXss6qyw- -server.ccl.net> X-Original-From: Alberto Sergio Garay Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Wed, 18 Jun 2008 08:06:02 -0300 MIME-Version: 1.0 Sent to CCL by: Alberto Sergio Garay [sgaray]-[fbcb.unl.edu.ar] Dear Dr. Ponder My name is Sergio Garay and I have been studying a small organic =20 molecule using FFE and Tinker's binaries and I have found some =20 problems which I can not understand and resolve. For example: running =20 a minimization routine (mm3 force field) I have obtained a =20 "reasonable" chemical structure, but using Monte Carlo minimization =20 program to search a global minimum (with 3 Argmstrong or 3 degrees as =20 step) I have got the molecule with the benzene ring distorted. If I =20 use a lesser step the program can do it well. Is there any explanation =20 for that? I thought that the routine always remembers the global =20 mininum, but in some point in the search it seems as it can't. Beside this when I run the "scan" routine, it asks me for an xyz =20 coordinates, which later (I think) transforms to internal z-matrix. =20 The problem is that the program works with internal coordinates and =20 some of the dihedrals are not properly defined, so it gives me a error =20 in some of the rotable bonds. Is there any way of giving a z-matrix as =20 input to the scan or montecarlo routine, where I can establish my own =20 dihedral angles?. I have tried every example given as Tinker examples, but no one give =20 any clue. Is there any Tinker list? where I can ask these kinds of =20 problems? . Thank you in advance. --=20 Dr. Sergio Garay Facultad de Bioquimica y Cs. Biol=F3gicas Universidad Nacional del Litoral Santa Fe - Argentina C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA Argentina Ph. +54 (342) 4575-213 Fax. +54 (342) 4575-221 From owner-chemistry@ccl.net Wed Jun 18 11:15:01 2008 From: "Peter Burger burger#,#chemie.uni-hamburg.de" To: CCL Subject: CCL: PESscan Message-Id: <-37178-080618110101-4338-zLrP9BhtLs7d5nt59tzycA++server.ccl.net> X-Original-From: Peter Burger Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 18 Jun 2008 17:00:29 +0200 MIME-Version: 1.0 Sent to CCL by: Peter Burger [burger+*+chemie.uni-hamburg.de] Dear Alcides, you are certainly right - the way you proposed is for sure better. The problem I encountered however, was that if one was approaching for instance linear structures with less well defined coordinates, each of the geometry points in this range was taking "for ever" in that the "loose" keyword was the way to go. Regards. Peter Alcides Simao alsimao{=}gmail.com schrieb: > Dear Alexandra, > Yes, you can do PES of uni, bi, tri, 'all-that-your-cpu-can-hold-as-long-as-it-doesn't-bust' dimensions ;) > Just be careful with the parameters you use to make the relaxed PES. > Peter mencioned also the use of the opt=loose for when some optimizations get stuck. It's a way of working, although I use a different approach. I reoptimize points that don't converge in a solo calculation, with the same converge criteria, for a longer time. IMHO, I get a tidier PES scan! Nevertheless, I will not dare to say that Peter way of working isn't correct - I just don't use it. Loose criteria means a less demanding convergence tolerance. But I'll try to use his way just to compare with mine, and see what I get. > Best Regards, > Alcides > > -- Prof. Dr. Peter Burger Institut fuer Anorganische und Angewandte Chemie Universitaet Hamburg Martin-Luther-King-Platz 6 D-20146 Hamburg Tel.:+49 040 42838 3662 FAX 6097 email: burger]_[chemie.uni-hamburg.de http://www.chemie.uni-hamburg.de/ac/AKs/Burger From owner-chemistry@ccl.net Wed Jun 18 12:09:01 2008 From: "Jose Duarte duarte!=!molgen.mpg.de" To: CCL Subject: CCL: rmsd calculation Message-Id: <-37179-080618055742-22347-/sJF2B0kYRkqBwnBe+4mmQ|a|server.ccl.net> X-Original-From: Jose Duarte Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 18 Jun 2008 11:25:04 +0200 MIME-Version: 1.0 Sent to CCL by: Jose Duarte [duarte ~ molgen.mpg.de] maxcluster does a very good job and very fast rmsd calculations. It also can do clustering using a few methods. I'm not sure though of the input formats, we have used it only with PDB files here. See http://www.sbg.bio.ic.ac.uk/~maxcluster/index.html Jose -- Jose M. Duarte Max Planck Institue for Molecular Genetics Berlin Antje Wolf antje.wolf(-)scai.fraunhofer.de wrote: > Sent to CCL by: "Antje Wolf" [antje.wolf]~[scai.fraunhofer.de] > Hi, > > I am looking for a (free) tool for calculating the RMSD between two molecule conformations, preferably a script or command line tool as I want to use it in batch mode. > It would be great if this tool also includes the possibility to do a clustering. > > Perhaps, someone has a good suggestion. > > Thanks in advance, > Antje> > > From owner-chemistry@ccl.net Wed Jun 18 12:44:01 2008 From: "Workalemahu Mikre Berhanu wberhanu|*|mail.ucf.edu" To: CCL Subject: CCL: Raman spectra using QM/MM Message-Id: <-37180-080617110321-26790-q+XsCNBNVF1FpHkD1ICebA]=[server.ccl.net> X-Original-From: "Workalemahu Mikre Berhanu" Date: Tue, 17 Jun 2008 11:03:17 -0400 Sent to CCL by: "Workalemahu Mikre Berhanu" [wberhanu|,|mail.ucf.edu] I was trying to use the QM/MM method for calculating the raman intensities using gauss view for linux. In the literature there are reports which show it is possible to do Raman intensity calculation using gaussuian. Could you please provide me information on how I could solve my problem? I have tried ONIOM(b3lyp:amber), ONIOM(b3lyp:uff) and ONIOM(b3lyp:dreiding) but I could not get the raman intensities. Thank you Sincerly From owner-chemistry@ccl.net Wed Jun 18 13:19:00 2008 From: "Mikolaj Feliks mikolaj.feliks/./pwr.wroc.pl" To: CCL Subject: CCL: rmsd calculation Message-Id: <-37181-080618061005-27050-BQi/b3kuMDxR9NvKKt1zxA]^[server.ccl.net> X-Original-From: Mikolaj Feliks Content-Disposition: inline Content-Type: multipart/mixed; boundary="envbJBWh7q8WU6mo" Date: Wed, 18 Jun 2008 11:32:23 +0200 MIME-Version: 1.0 Sent to CCL by: Mikolaj Feliks [mikolaj.feliks[a]pwr.wroc.pl] --envbJBWh7q8WU6mo Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Hi, here is my simple python script that takes 2 molecules in a standard xyz format and calculates rmsd. Optionally, the calculation can be limited to the particular atom pairs. See comments inside for details. Unfortunately, it does not support clustering, just compares 2 molecules. Good luck, mfx On Wed, Jun 18, 2008 at 04:10:07AM -0400, Antje Wolf antje.wolf(-)scai.fraunhofer.de wrote: > > Sent to CCL by: "Antje Wolf" [antje.wolf]~[scai.fraunhofer.de] > Hi, > > I am looking for a (free) tool for calculating the RMSD between two molecule conformations, preferably a script or command line tool as I want to use it in batch mode. > It would be great if this tool also includes the possibility to do a clustering. > > Perhaps, someone has a good suggestion. > > Thanks in advance, > Antje -\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\- Mikolaj Feliks Molecular Modeling & Quantum Chemistry Group Institute of Physical & Theoretical Chemistry Wroclaw University of Technology, Poland http://ichfit.ch.pwr.wroc.pl/?q=user/81 -\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\- --envbJBWh7q8WU6mo Content-Type: text/x-python; charset=us-ascii Content-Disposition: attachment; filename="rms.py" #!/usr/bin/env python # description: calculates RMS of two molecules stored in xyz format # REQUIREMENTS: # + the same number of atoms # + identical order of atoms within xyz files > from sys import argv, exit > from math import sqrt def load_file(filename, t): p = open(filename, "r") n = int(p.readline().strip()) p.readline() for i in range(0, n): v = p.readline().strip().split() x = float(v[1]) y = float(v[2]) z = float(v[3]) t.append([x, y, z]) p.close() #--------------------------------------------------------------------- # RMS = sqrt(1/N * sigma((xai-xbi)**2 + (yai-ybi)**2 + (zai-zbi)**2)) def calc_RMS(t1, t2): t = 0.0 N = len(t1) for i in range(0, N): x1 = t1[i][0] y1 = t1[i][1] z1 = t1[i][2] x2 = t2[i][0] y2 = t2[i][1] z2 = t2[i][2] dx = x1 - x2 dy = y1 - y2 dz = z1 - z2 t += (dx**2 + dy**2 + dz**2) return sqrt(t / N) #--------------------------------------------------------------------- largv = len(argv) if largv < 3: print("USAGE: rms.py file1.xyz file2.xyz [atom1 [atom2 [...]]]") exit() tab1 = [] load_file(argv[1], tab1) tab2 = [] load_file(argv[2], tab2) if largv > 3: atom_tab = [] for i in range(3, largv): atom_tab.append(int(argv[i])) mtab1 = [] for i in range(0, len(tab1)): for a in atom_tab: if i == (a - 1): mtab1.append(tab1[i]) mtab2 = [] for i in range(0, len(tab2)): for a in atom_tab: if i == (a - 1): mtab2.append(tab2[i]) print("RMS of atoms "), for a in atom_tab: print("%d " % a), mRMS = calc_RMS(mtab1, mtab2) print("= %.8f" % mRMS) else: RMS = calc_RMS(tab1, tab2) print("RMS = %.8f" % RMS) --envbJBWh7q8WU6mo-- From owner-chemistry@ccl.net Wed Jun 18 13:53:01 2008 From: "Jerome Kieffer jerome.Kieffer()terre-adelie.org" To: CCL Subject: CCL: rmsd calculation Message-Id: <-37182-080618133238-27267-0X5ofbA/di9P722Br2ihdw:-:server.ccl.net> X-Original-From: Jerome Kieffer Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-15 Date: Wed, 18 Jun 2008 19:32:04 +0200 Mime-Version: 1.0 Sent to CCL by: Jerome Kieffer [jerome.Kieffer||terre-adelie.org] > I am looking for a (free) tool for calculating the RMSD between two molec= ule conformations, preferably a script or command line tool as I want to us= e it in batch mode. > It would be great if this tool also includes the possibility to do a clus= tering. >=20 > Perhaps, someone has a good suggestion. search for the Kabsch algorythm ... http://en.wikipedia.org/wiki/Kabsch_algorithm I implemented it in python for CAChe files, if you are intersted in. One tip for clustering: you can sort your vector-set by type of atoms and distance to the barycenter to overcome the limitation that your atoms could have diferent names (can be due to internal symmetries). =20 Best regards --=20 J=E9r=F4me KIEFFER : http://www.terre-adelie.org =C0 v=E9lo, prendre une rue =E0 contre-sens est moins dangeureux que prendre un boulevard dans le sens l=E9gal. =C0 qui la faute ? From owner-chemistry@ccl.net Wed Jun 18 15:34:01 2008 From: "Antonio G De Crisci antonio.decrisci[*]utoronto.ca" To: CCL Subject: CCL:G: Frequency Vs Hessian Message-Id: <-37183-080618152838-22539-8q6PEwwI/YYSVc51x9NtTQ{:}server.ccl.net> X-Original-From: "Antonio G De Crisci" Date: Wed, 18 Jun 2008 15:28:34 -0400 Sent to CCL by: "Antonio G De Crisci" [antonio.decrisci^^^utoronto.ca] Hello, Can somebody tell me the difference between a frequency calculation in Gaussian compared to a hessian calculation (with vibrational analysis) in PC GAMESS? Also, in GAMESS, when performing a hessian, I have two method options: numeric or analytic. When I choose the numeric size, I have an option of changing the displacement size. What is the difference between the two, and what value of the displacement size (default= 0.01) would be suitable for a B3LYP/6-311G. Thanks, Antonio De Crisci University of Toronto From owner-chemistry@ccl.net Wed Jun 18 16:08:00 2008 From: "Steve Williams willsd]|[appstate.edu" To: CCL Subject: CCL:G: Raman spectra using QM/MM Message-Id: <-37184-080618151655-21337-9aI+TdHefOa3avoPRmHMNQ()server.ccl.net> X-Original-From: Steve Williams Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 18 Jun 2008 14:17:41 -0400 MIME-Version: 1.0 Sent to CCL by: Steve Williams [willsd^_^appstate.edu] Raman intensities are available in G03, but since they require numerical derivatives for MP2 and DFT methods they are very slow to compute and by default they are not calculated on a frequency job. If you change your input to include freq=raman on the route line, they will be computed. Six separate calculations will be done for each atom (+/- displacements in x, y, z) to compute the needed polarizability derivatives. You can estimate how long this will take by doing a single point polarizability calculation then multiplying the time required for this by 6*N where N is the number of atoms in your molecule (the portion you want to compute with b3lyp). Caveat: While I have computed LOTS of Raman spectra with Gaussian, I have not combined this with an ONIOM calculation.... maybe it does not work at all with ONIOM. BTW: If you include the first 20 or so lines of your input file when posting a question like this, you are more likely to get useful answers. For example I am just assuming that you did not specify freq=raman. Steve Williams Workalemahu Mikre Berhanu wberhanu|*|mail.ucf.edu wrote: > Sent to CCL by: "Workalemahu Mikre Berhanu" [wberhanu|,|mail.ucf.edu] > > I was trying to use the QM/MM method for calculating the raman intensities using gauss view for linux. In the literature there are reports which show it is possible to do Raman intensity calculation using gaussuian. Could you please provide me information on how I could solve my problem? I have tried ONIOM(b3lyp:amber), ONIOM(b3lyp:uff) and ONIOM(b3lyp:dreiding) but I could not get the raman intensities. > > > Thank you > > Sincerly> > > From owner-chemistry@ccl.net Wed Jun 18 16:43:00 2008 From: "Ol Ga eurisco1,+,pochta.ru" To: CCL Subject: CCL:G: AMD Phenom vs. Intel Quad Q6600 Message-Id: <-37185-080618162053-19995-eehSQPooS8qklMXfOjaEPg%x%server.ccl.net> X-Original-From: "Ol Ga" Date: Wed, 18 Jun 2008 16:20:49 -0400 Sent to CCL by: "Ol Ga" [eurisco1**pochta.ru] Hello all, Does anybody know some tests about performance of running Gaussian calculation on 4-core CPUs : AMD Phenom vs. Intel Quad Q6600 via shared memory? Any comments are highly appreciated. Thank you very much in advance. Ol Ga From owner-chemistry@ccl.net Wed Jun 18 17:18:01 2008 From: "Alcides Simao alsimao ~ gmail.com" To: CCL Subject: CCL:G: Frequency Vs Hessian Message-Id: <-37186-080618164630-6251-Po7VVrXiOm/fIOnJYe5r7w-.-server.ccl.net> X-Original-From: "Alcides Simao" Content-Type: multipart/alternative; boundary="----=_Part_5977_24421070.1213821960351" Date: Wed, 18 Jun 2008 21:46:00 +0100 MIME-Version: 1.0 Sent to CCL by: "Alcides Simao" [alsimao#,#gmail.com] ------=_Part_5977_24421070.1213821960351 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear Antonio, IMHO, the basis of both GAUSSIAN and GAMESS vibrational analysis is the same. Numerical and analytical only have to do to the way the equations are solved. Analytical is not always a choice! It depends on the system. Just remind something: The only system that can be completely solved analytically is the hydrogen system :) All other are approximations. Numerical comes in when analytical fails! But be careful! Changing displacements can lead to trouble. I recommend you to read a general computational chemistry book. They explain this methods in great detail, in a compreensive way. And also - read the program's manual! This last paragraph reminds me to read further on the subject : I'm extremely green on it :o) Best, Alcides ------=_Part_5977_24421070.1213821960351 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear Antonio,

IMHO, the basis of both GAUSSIAN and GAMESS vibrational analysis is the same.

Numerical and analytical only have to do to the way the equations are solved. Analytical is not always a choice! It depends on the system. Just remind something: The only system that can be completely solved analytically is the hydrogen system :) All other are approximations.
Numerical comes in when analytical fails!

But be careful! Changing displacements can lead to trouble. I recommend you to read a general computational chemistry book. They explain this methods in great detail, in a compreensive way. And also - read the program's manual!

This last paragraph reminds me to read further on the subject : I'm extremely green on it :o)

Best,

Alcides
------=_Part_5977_24421070.1213821960351-- From owner-chemistry@ccl.net Wed Jun 18 17:54:00 2008 From: "Peter Burger burger-$-chemie.uni-hamburg.de" To: CCL Subject: CCL:G: Raman spectra using QM/MM Message-Id: <-37187-080618171404-7916-kMZMi2kRTKTkVxSSz5f/hg###server.ccl.net> X-Original-From: Peter Burger Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 18 Jun 2008 23:13:27 +0200 MIME-Version: 1.0 Sent to CCL by: Peter Burger [burger^chemie.uni-hamburg.de] I would suggest to have a look at Turbomole ver. 5.10 which offers _analytical_ Raman intensities. Including the very fast RI DFT methods even sizable molecules are amenable for these calculations without the need for ONIOM unless we are talking about proteins. Just worth my .01 cents Peter Steve Williams willsd]|[appstate.edu schrieb: > > Sent to CCL by: Steve Williams [willsd^_^appstate.edu] > Raman intensities are available in G03, but since they require > numerical derivatives for MP2 and DFT methods they are very slow to > compute and by default they are not calculated on a frequency job. If > you change your input to include freq=raman on the route line, they > will be computed. Six separate calculations will be done for each > atom (+/- displacements in x, y, z) to compute the needed > polarizability derivatives. You can estimate how long this will take > by doing a single point polarizability calculation then multiplying > the time required for this by 6*N where N is the number of atoms in > your molecule (the portion you want to compute with b3lyp). > > Caveat: While I have computed LOTS of Raman spectra with Gaussian, I > have not combined this with an ONIOM calculation.... maybe it does not > work at all with ONIOM. > > BTW: If you include the first 20 or so lines of your input file when > posting a question like this, you are more likely to get useful > answers. For example I am just assuming that you did not specify > freq=raman. > > Steve Williams > > > Workalemahu Mikre Berhanu wberhanu|*|mail.ucf.edu wrote: >> Sent to CCL by: "Workalemahu Mikre Berhanu" [wberhanu|,|mail.ucf.edu] >> >> I was trying to use the QM/MM method for calculating the raman >> intensities using gauss view for linux. In the literature there are >> reports which show it is possible to do Raman intensity calculation >> using gaussuian. Could you please provide me information on how I >> could solve my problem? I have tried ONIOM(b3lyp:amber), >> ONIOM(b3lyp:uff) and ONIOM(b3lyp:dreiding) but I could not get the >> raman intensities. >> >> >> Thank you >> >> Sincerlyhttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > -- Prof. Dr. Peter Burger Institut fuer Anorganische und Angewandte Chemie Universitaet Hamburg Martin-Luther-King-Platz 6 D-20146 Hamburg Tel.:+49 040 42838 3662 FAX 6097 email: burger%a%chemie.uni-hamburg.de http://www.chemie.uni-hamburg.de/ac/AKs/Burger From owner-chemistry@ccl.net Wed Jun 18 19:39:00 2008 From: "zhendong zhao zzhao]![olemiss.edu" To: CCL Subject: CCL:G: AMD Phenom vs. Intel Quad Q6600 Message-Id: <-37188-080618193351-18669-o7KS2wZGxnoXTqeCarACbA!^!server.ccl.net> X-Original-From: zhendong zhao Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII Date: Wed, 18 Jun 2008 17:36:44 -0500 Mime-Version: 1.0 Sent to CCL by: zhendong zhao [zzhao:-:olemiss.edu] Hi, In brief, gaussian G03 E01 does not support phenom CPU currently. Please read gaussian company notice on AMD phenom CPU. I already had the bad experience on phenom 9850. I made some unofficial comments on it. I just run simple benchmark tests, so please DO NOT use my comments to make your final decision. G03 parallel calculations are impossible on Phenom CPU now, the OS will hang/dead-lock when you run G03 parallel calculations. The benchmark on a single core CPU G03 calculation is still not promising for phenom, almost as fast as Q6600. I do not think phenom CPU is as fast as Intel Q6600 for gamess. I compared running gamess on phenom 9850 with Q6600, the result is not promising for AMD phenom. I use gcc and blas-goto to do the test. BTW, I am not sure whether the known TLB bug in AMD quad core CPU is fixed or not, even it is supposed already fixed. The bug will make troubles when you are doing parallel calculations. Linux runs stable on AMD phenom CPUs, the unstabilities is from parallel calculations. Warning, My benchmark tests are too simple, please DO NOT use it as your final decision. Best regards, ZZ On Wed, 18 Jun 2008 16:20:49 -0400 "Ol Ga eurisco1,+,pochta.ru" wrote: > > Sent to CCL by: "Ol Ga" [eurisco1**pochta.ru] > Hello all, > > Does anybody know some tests about performance of running Gaussian > calculation on 4-core CPUs : AMD Phenom vs. Intel Quad Q6600 via > shared memory? > > Any comments are highly appreciated. > Thank you very much in advance. > > Ol Ga > > > > -= This is automatically added to each message by the mailing script > =- To recover the email address of the author of the message, please > change the strange characters on the top line to the !^! sign. You can > also> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > From owner-chemistry@ccl.net Wed Jun 18 21:02:00 2008 From: "Hod Greeley hod-ccl+/-greeley.org" To: CCL Subject: CCL:G: Frequency Vs Hessian Message-Id: <-37189-080618195536-26698-qise0Gz7URuEZlH9YOj19A[-]server.ccl.net> X-Original-From: "Hod Greeley" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Wed, 18 Jun 2008 14:44:26 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: "Hod Greeley" [hod-ccl~~greeley.org] In this instance, analytic would refer to being able to derive closed form expressions for the derivatives of the energy with respect to coordinate changes in whatever approximation method you're using (Hartree-Fock, MP2, etc). In contrast, numeric derivatives calculate approximate values for the derivatives by calculating the energy using slight differences in the coordinates and performing the appropriate simple algebra. Numeric techniques only require the ability to perform the energy calculation itself. This would be preferred if either you simply don't have an expression for the analytic derivatives, or they are overly costly to calculate compared to the energy alone. As for the displacement, in theory the smaller the value the better. That's only true, though, if your calculations are exact. But, of course, computers don't calculate to infinite precision. So, the displacement you choose would need to balance error introduced by a larger displacement against round off problems. There's more to this kind of calculation than that, too. You have basis set superposition errors to consider, for one. In short, depending on what your goal is, it may be risky to just set some parameters and blindly use the results. I'm sure others here can give you more specific pointers if you describe what you're trying to achieve in more detail. Best, Hod > Dear Antonio, > > IMHO, the basis of both GAUSSIAN and GAMESS vibrational analysis is the > same. > > Numerical and analytical only have to do to the way the equations are > solved. Analytical is not always a choice! It depends on the system. Just > remind something: The only system that can be completely solved > analytically > is the hydrogen system :) All other are approximations. > Numerical comes in when analytical fails! > > But be careful! Changing displacements can lead to trouble. I recommend > you > to read a general computational chemistry book. They explain this methods > in > great detail, in a compreensive way. And also - read the program's manual! > > This last paragraph reminds me to read further on the subject : I'm > extremely green on it :o) > > Best, > > Alcides > From owner-chemistry@ccl.net Wed Jun 18 21:42:01 2008 From: "Francisco Hernandez-Guzman fhernand=accelrys.com" To: CCL Subject: CCL: Materials studio: Any idea about the cost? Message-Id: <-37190-080617132137-13685-HVHmSqU/0XKcEjNkXQkdcw]![server.ccl.net> X-Original-From: "Francisco Hernandez-Guzman" Content-Type: multipart/alternative; boundary="----=_Part_330_11716312.1213721516500" Date: Tue, 17 Jun 2008 09:51:56 -0700 MIME-Version: 1.0 Sent to CCL by: "Francisco Hernandez-Guzman" [fhernand .. accelrys.com] ------=_Part_330_11716312.1213721516500 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi Kass, The price can vary depending on what you're interested on doing. The price also depends on whether you're in academia/non-profit or commercial. Please send me an email directly so I can get you in touch with the right person to provide you with a quote. Kind regards, Francisco ------------------------------------------------------------------- Francisco G. Hernandez-Guzman, Ph.D. Lead Solutions Scientist, Protein Modeling, Simulations and X-ray - USA Accelrys Inc. (http://www.accelrys.com) Office: (858) 799 - 5606 Fax: (858) 799 - 5100 Mobile: (858) 361 - 3020 E-mail: fhernandez- -accelrys.com -------------------------------------------------------------------- Accelrys support: 1-800-756-4674 E-mail: support- -accelrys.com On 6/16/08, Kaci Tizi_Ouzou kaci.tiziouzou#,#gmail.com < owner-chemistry- -ccl.net> wrote: > > Hi all, > > > Just wondering whether anyone has any idea (roughly) about the cost of > Materials Studio. > > Cheers > > > Kass > ------=_Part_330_11716312.1213721516500 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Hi Kass,
 
The price can vary depending on what you're interested on doing.  The price also depends on whether you're in academia/non-profit or commercial.
 
Please send me an email directly so I can get you in touch with the right person to provide you with a quote.
 
Kind regards,
 
Francisco
 
-------------------------------------------------------------------
Francisco G. Hernandez-Guzman, Ph.D.
Lead Solutions Scientist, Protein Modeling, Simulations and X-ray - USA
Accelrys Inc. (http://www.accelrys.com)
Office: (858) 799 - 5606
Fax: (858) 799 - 5100
Mobile: (858) 361 - 3020
E-mail: fhernandez- -accelrys.com
--------------------------------------------------------------------
Accelrys support: 1-800-756-4674
E-mail: support- -accelrys.com

 
On 6/16/08, Kaci Tizi_Ouzou kaci.tiziouzou#,#gmail.com <owner-chemistry- -ccl.net> wrote:
Hi all,


Just wondering whether anyone has any idea (roughly) about the cost of Materials Studio.

Cheers


Kass

------=_Part_330_11716312.1213721516500-- From owner-chemistry@ccl.net Wed Jun 18 22:20:00 2008 From: "Vincenzo Verdolino vincenzo.verdolino=nemo.unipr.it" To: CCL Subject: CCL:G: Frequency Vs Hessian Message-Id: <-37191-080618181819-27641-cgIPmmfnc+Fc+zA9DbKefg-*-server.ccl.net> X-Original-From: "Vincenzo Verdolino" Content-Type: text/plain; charset=iso-8859-1 Date: Wed, 18 Jun 2008 23:39:32 +0200 MIME-Version: 1.0 Sent to CCL by: "Vincenzo Verdolino" [vincenzo.verdolino,+,nemo.unipr.it] Hi the frequencies calculation is an Hessian computation, i.e. the Second partial derivative of the potential energy V with respect to displacement of the atoms in Cartesian coordinates (CART). This matrix 3Nx3N can be evaluated by a numerical or analytical approach. In the first case, you compute the analytical first derivative of the potential for a given set of 3N coordinates and you will do again for another set of 3N coordinates displaced by a finite step (e.g. 0.01). In the second case you will run also the second derivative with an analytical expression if available (for the most common level of theory are this is available) Unless you need to develop other analytical second derivatives or for other particular porpoise I suggest you the analytical way cause it is standard and faster. more details at http://www.gaussian.com/g_whitepap/vib.htm Vincenzo Verdolino On Wed, 18 Jun 2008 15:28:34 -0400, Antonio G De Crisci antonio.decrisci[*] utoronto.ca wrote > Sent to CCL by: "Antonio G De Crisci" > [antonio.decrisci^^^utoronto.ca] Hello, > > Can somebody tell me the difference between a frequency calculation > in Gaussian compared to a hessian calculation (with vibrational > analysis) in PC GAMESS? > > Also, in GAMESS, when performing a hessian, I have two method > options: numeric or analytic. When I choose the numeric size, I have > an option of changing the displacement size. What is the difference > between the two, and what value of the displacement size (default= > 0.01) would be suitable for a B3LYP/6-311G. > > Thanks, > Antonio De Crisci > University of Toronto > > -= This is automatically added to each message by the mailing script > =- To recover the email address of the author of the message, please > change the strange characters on the top line to the . sign. You can > also> > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)-- Universita' degli Studi di Parma (http://www.unipr.it) From owner-chemistry@ccl.net Wed Jun 18 22:52:01 2008 From: "frisch..gaussian.com (Michael Frisch)" To: CCL Subject: CCL:G: Raman spectra using QM/MM Message-Id: <-37192-080618211048-1581-DhvkCYMZPYuc+pChcLNVDw[#]server.ccl.net> X-Original-From: frisch^gaussian.com (Michael Frisch) Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Wed, 18 Jun 2008 20:19:20 -0400 Mime-Version: 1.0 Sent to CCL by: frisch^_^gaussian.com (Michael Frisch) On Wed, Jun 18, 2008 at 02:17:41PM -0400, Steve Williams willsd]|[appstate.edu wrote: > > Sent to CCL by: Steve Williams [willsd^_^appstate.edu] > Raman intensities are available in G03, but since they require numerical > derivatives for MP2 and DFT methods they are very slow to compute and by > default they are not calculated on a frequency job. If you change your > input to include freq=raman on the route line, they will be computed. > Six separate calculations will be done for each atom (+/- displacements > in x, y, z) to compute the needed polarizability derivatives. You can > estimate how long this will take by doing a single point polarizability > calculation then multiplying the time required for this by 6*N where N > is the number of atoms in your molecule (the portion you want to compute > with b3lyp). > This is not correct. In G03, MP2 and B3LYP Raman intensities (static polarizability derivatives, "Freq=Raman" on the route card) are done by numerically differentiating the analytic dipole derivatives with respect to an applied electric field. So there are only 6 additional calculations regardless of the size of the molecule. The cost of each of the 6 calculations in a finite electric field is somewhat more than a polarizability calculation but much less than the calculation of the second derivatives for the basic frequency calculation. So for very small molecules the total cost of Freq=Raman with DFT or MP2 is around than 3x the cost of just doing Freq, but this drops to 1.5x for larger systems. Freq=Raman does work with ONIOM. With ONIOM(MO:MM) and mechanical embedding the cost is about the same as for the MO calculation on the model system. With ONIOM(MO:MM) and electronic embedding, the cost is higher than just doing the model system (with or without Raman) because derivatives with respect to all the nuclei have to be included in the QM calculation. Mike Frisch