From owner-chemistry@ccl.net Mon Feb 27 02:17:01 2012 From: "cina foroutan canyslopus||yahoo.co.uk" To: CCL Subject: CCL: How to check if molecule has dissociated? Message-Id: <-46382-120227021014-5529-GsyM0a05gkrt1AbOzjm9Zw(~)server.ccl.net> X-Original-From: cina foroutan Content-Type: multipart/alternative; boundary="1429413389-643035872-1330326607=:14463" Date: Mon, 27 Feb 2012 07:10:07 +0000 (GMT) MIME-Version: 1.0 Sent to CCL by: cina foroutan [canyslopus=yahoo.co.uk] --1429413389-643035872-1330326607=:14463 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Dima,=0A=0AYour question is not naive! It is a fundamental question. T= here are various approaches in chemistry for analyzing the nature of bondin= g. You can test your molecule by either of them but be aware that you may c= ome to different results based on the approach that you select. You must fi= rst decide to use one of them. Valence Bond approach, NBO analysis, QTAIM a= nalysis, ELF analysis... Which one is your favorite?=0AI myself answer this= question in terms of the QTAIM approach. You can simply measure the extent= of electron exchange (electron delocalization) within the context of QTAIM= and decide whether the bond is covalent or it has very few covalency. In a= normal single bond usually "one" electron is shared between two atoms; mea= sure it in your molecule in the absence of electric field at first. When yo= u apply the electric field,the electron exchange will change. You should me= asure it again and compare the new value with the former. Now you can quant= ify the extent of covalency compared with the field free condition.=0AYou s= hould be aware that even an ionic bond is a chemical bond. So heedfully mea= sure the atomic charges and energies of the bonded atoms in presence and ab= sence of the field but be careful with interpretation of the results!=A0=0A= Finally, I have to mention that you can do all these computations in two st= eps: (1) preparing a WFN or WFX file by your software then (2) analysing th= e results by the AIMAll suite of programs (http://aim.tkgristmill.com).=0A= =0A=0AGood luck,=0ACina=0A=0A=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=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=0ACina Foroutan-Nejad, Ph. D.=0ASchool of= Chemistry,=0AUniversity College of Science,=0AUniversity of Tehran, Tehran= , Iran=0Ahttp://independent.academia.edu/CinaForoutanNejad=0A=0A=0A=0A=0A__= ______________________________=0A From: Dima Koroliov dimajungle]*[gmail.co= m =0ATo: "Foroutan-Nejad, Cina " =0ASent: Monday, 27 February 2012, 3:05=0ASubject: CCL: How= to check if molecule has dissociated?=0A =0A=0ASent to CCL by: "Dima=A0 Ko= roliov" [dimajungle*o*gmail.com]=0AHello,=0A=0APlease forgive me my naive q= uestion. I am performing some calculations of an organic molecule under eex= ternal lectric field. I am performing the geometry optimization followed by= vibrational analysis and want to look into the molecular properties. Could= you suggest me how to simply check whether the molecule is dissociated or = not? I observe the significant elongation of one of the bonds, shift of the= related vibrational frequencies, a progressive increase of the dipole mome= nt value, upper shift of the homo orbital energy. However, I cannot decide = it it is still one molecule or is there are two dissociated fragments? =0A= =0ARegards,=0ADima=0A=0A=0A=0A-=3D This is automatically added to each mess= age by the mailing script =3D-=0ATo recover the email address of the author= of the message, please change=0Athe strange characters on the top line to = the %a% sign. You can also=0Alook up the X-Original-From: line in the mail he= ader.=0A=0A=0A=A0 =A0 =A0 h= ttp://www.ccl.net/cgi-bin/ccl/send_ccl_message=0A=0AE-mail to administrator= s: CHEMISTRY-REQUEST%a%ccl.net or use=0A=A0 =A0 =A0 http://www.ccl.net/cgi-bi= n/ccl/send_ccl_message=0A=0A=0A=A0 =A0 =A0 http://ww= w.ccl.net/chemistry/sub_unsub.shtml=0A=0ABefore posting, check wait time at= : http://www.ccl.net=0A=0A=0AConferences: http= ://server.ccl.net/chemistry/announcements/conferences/=0A=0ASearch Messages= : http://www.ccl.net/chemistry/searchccl/index.shtml=0A=0AIf your mail boun= ces from CCL with 5.7.1 error, check:=0A=A0 =A0 =A0 http://www.ccl.net/spam= mers.txt=0A=0A--1429413389-643035872-1330326607=:14463 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Dima,

Your question is not naive! It is = a fundamental question. There are various approaches in chemistry for analy= zing the nature of bonding. You can test your molecule by either of them bu= t be aware that you may come to different results based on the approach tha= t you select. You must first decide to use one of them. Valence Bond approa= ch, NBO analysis, QTAIM analysis, ELF analysis... Which one is your favorit= e?
I myself answer this question in terms of the QTA= IM approach. You can simply measure the extent of electron exchange (electr= on delocalization) within the context of QTAIM and decide whether the bond = is covalent or it has very few covalency. In a normal single bond usually "= one" electron is shared between two atoms; measure it in your molecule in the absence of electric field at first. When you apply the electric fie= ld,the electron exchange will change. You should measure it again and compa= re the new value with the former. Now you can quantify the extent of covale= ncy compared with the field free condition.
You shou= ld be aware that even an ionic bond is a chemical bond. So heedfully measur= e the atomic charges and energies of the bonded atoms in presence and absen= ce of the field but be careful with interpretation of the results! 
Finally, I have to mention that you can do all these c= omputations in two steps: (1) preparing a WFN or WFX file by your software = then (2) analysing the results by the AIMAll suite of programs (http://aim.tkgristmill.com).

Good luck,
Cina

=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=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
Cina Foroutan-Nejad, Ph. D.
Sch= ool of Chemistry,
University College of Science,
University of Tehran, Tehran, Iran
http://independent.academia.edu/CinaForoutanNejad


From: Dima Ko= roliov dimajungle]*[gmail.com <owner-chemistry%a%ccl.net>
To: "Foroutan-Nejad, Cina "= <canyslopus%a%yahoo.co.uk>
= Sent: Monday, 27 February 2012, 3:05
Subject: CCL: How to check if molecule has dissoc= iated?


Sent to CCL by: "Dima  Koroliov" [di= majungle*o*gmail.com]
Hello,

Please forgive me my naive question.= I am performing some calculations of an organic molecule under eexternal l= ectric field. I am performing the geometry optimization followed by vibrati= onal analysis and want to look into the molecular properties. Could you sug= gest me how to simply check whether the molecule is dissociated or not? I o= bserve the significant elongation of one of the bonds, shift of the related vibrational frequencies, a progressive increase of the dipole moment value= , upper shift of the homo orbital energy. However, I cannot decide it it is= still one molecule or is there are two dissociated fragments?

Rega= rds,
Dima



-=3D This is automatically added to each messag= e by the mailing script =3D-
To recover the email address of the author = of the message, please change
the strange characters on the top line to = the %a% sign. You can also
look up the X-Original-From: line in the mail h= eader.

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--1429413389-643035872-1330326607=:14463-- From owner-chemistry@ccl.net Mon Feb 27 05:36:01 2012 From: "hreis[a]eie.gr hreis[a]eie.gr" To: CCL Subject: CCL:G: single point calculations and g09/l508.exe and g09/l502.exe errors Message-Id: <-46383-120227044922-7572-yp320a2WOGSuUhiCtcU13A*_*server.ccl.net> X-Original-From: "hreis-x-eie.gr" Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=iso-8859-1 Date: Mon, 27 Feb 2012 04:49:57 -0500 MIME-Version: 1.0 Sent to CCL by: "hreis^-^eie.gr" [hreis^-^eie.gr] Hi Reza, You could try the standard scf (no qc) with integral=ultrafine scf=noincfock and leave out 6D 10F. Sometimes nosymm also helps. Heribert Original Message: ----------------- > From: Reza Shojaei shojaei81#gmail.com owner-chemistry,ccl.net Date: Sun, 26 Feb 2012 13:52:31 -0500 To: hreis,eie.gr Subject: CCL:G: single point calculations and g09/l508.exe and g09/l502.exe errors Sent to CCL by: " Reza Shojaei" [shojaei81,+,gmail.com] Thanks for suggestions, but none of them are working. does anyone have new Idea? > "eurisco1::pochta.ru" wrote: > > Sent to CCL by: [eurisco1(_)pochta.ru] > Dear Reza Shojaei, > > > I guess that keywords SCF(XQC,vshift=150,maxcycle=512) will be helpful. > > Sincerely, > Ol Ga > > > > ----- ----- > > From: Reza Shojaei shojaei81[-]gmail.com > Sent: Friday, February 24, 2012 11:15 AM > To: Ga, Ol > Subject: CCL:G: single point calculations and g09/l508.exe and g09/l502.exe > errors > > > Sent to CCL by: "Reza Shojaei" [shojaei81],[gmail.com] > Yes, there is more explanations on the errors. > > for g09/l502 I got this message: > > Convergence failure -- run terminated. > Error termination via Lnk1e in .../g09/l502.exe > > and for g09/l508.exe the message was: > > Search did not lower the energy significantly. > No lower point found -- try reversing direction. > Search did not lower the energy significantly. > No lower point found -- switch to scaled steepest descent. > Search did not lower the energy significantly. > Scaled steepest descent with Shift=0.000 failed. > Search did not lower the energy significantly. > Scaled steepest descent with Shift=0.025 failed. > Search did not lower the energy significantly. > Scaled steepest descent with Shift=0.050 failed. > Search did not lower the energy significantly. > Scaled steepest descent with Shift=0.075 failed. > Search did not lower the energy significantly. > No lower point found -- switch to steepest descent. > Search did not lower the energy significantly. > Search did not lower the energy significantly. > Search did not lower the energy significantly. > No lower point found -- run aborted. > Error termination via Lnk1e in ...../g09/l508.exe > > Reza > > > "Dr. Vitaly V. Chaban vvchaban**gmail.com" wrote: > > > > Sent to CCL by: "Dr. Vitaly V. Chaban" [vvchaban]^[gmail.com] > > I suppose there should be more specific descriprion of your problem(s) > > than just "g09/l508.exe and g09/l502.exe". > > > > -- > > Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. > > Univ. Rochester, Rochester, New York 14627-0216 > > THE UNITED STATES OF AMERICA > > > > > > > > > > On Thu, Feb 23, 2012 at 4:20 PM, Reza Shojaei shojaei81.:.gmail.com > > wrote: > > > > > > Sent to CCL by: " Reza Shojaei" [shojaei81*gmail.com] > > > Dear all, > > > > > > I do single point calculations on Biphenyl by Gaussian 09 using HPC but > > > I > > > have encountered with serious problems and all my attempts failed and I > > > get > > > g09/l508.exe and g09/l502.exe error messages. I have tried different > > > keywords like scf=tight, scf(maxcycle=300), L508, scf=fermi, scf=xqc and > > > scf=qc, but none of them succeed. does someone have any Idea to overcome > > > this > > > problem. your suggestions are highly appreciated.the input file is : > > > > > > %nproc=8 > > > %mem=8gb > > > # b3lyp/aug-cc-pvdz 6d 10f POP=FULL GFINPUT scf=qc > > > > > > Biphenyl twisted b3lyp mometum distribution > > > > > > 0 1 > > > C 0.000000 0.000000 0.723101 > > > C 0.000000 0.000000 -0.723101 > > > C -0.158093 1.217136 1.466542 > > > C -0.158093 -1.217136 -1.466542 > > > C 0.158093 -1.217136 1.466542 > > > C 0.158093 1.217136 -1.466542 > > > C -0.166057 1.211550 2.847549 > > > C 0.166057 -1.211550 2.847549 > > > C -0.166057 -1.211550 -2.847549 > > > C 0.166057 1.211550 -2.847549 > > > C 0.000000 0.000000 3.549464 > > > C 0.000000 0.000000 -3.549464 > > > H -0.309412 2.160499 0.944666 > > > H 0.309412 -2.160499 0.944666 > > > H -0.309412 -2.160499 -0.944666 > > > H 0.309412 2.160499 -0.944666 > > > H -0.304449 2.143962 3.396690 > > > H -0.304449 -2.143962 -3.396690 > > > H 0.304449 2.143962 -3.396690 > > > H 0.304449 -2.143962 3.396690 > > > H 0.000000 0.000000 4.641585 > > > H 0.000000 0.000000 -4.641585 > > > > > > > > > Rezahttp://www.ccl.net/cgi- bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://w ww. ccl.net/spammers.txthttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt-------------------------------------------------------------------- myhosting.com - Premium Microsoft® Windows® and Linux web and application hosting - http://link.myhosting.com/myhosting From owner-chemistry@ccl.net Mon Feb 27 07:45:00 2012 From: "=?ISO-8859-1?Q?Jo=E3o_Henriques?= joao.henriques.32353:+:gmail.com" To: CCL Subject: CCL:G: Gaussian input file command Message-Id: <-46384-120227074254-11089-LnQr5Pgk1qXtSiQI0Y5rVQ^server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Jo=E3o_Henriques?= Content-Type: multipart/alternative; boundary=e89a8f83ab7d8f491d04b9f172a1 Date: Mon, 27 Feb 2012 13:42:47 +0100 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Jo=E3o_Henriques?= [joao.henriques.32353 : gmail.com] --e89a8f83ab7d8f491d04b9f172a1 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Sergio, Post the error please (tail the output file and post it here). And yes, of course G03 supports solvation... Best regards, Joao On Sat, Feb 25, 2012 at 3:47 PM, sergio.manzetti]~[gmail.com < owner-chemistry::ccl.net> wrote: > Dear CCLers, I get an error message upon trying to batch a job to Gaussia= n > 03 with solvation parameters: > > %nproc=3D4 > %Mem=3D1900MB > #P MPW1PW91/6-311+G(d)/auto scrf=3D(solvent=3Dwater) guess=3Dsave polar # > # Opt > # polar > # Gfinput IOP(6/7=3D3) Pop=3Dfull Density Test > # Units(Ang,Deg) > > > Does G03 support solvation at all? > > All the best > > > Sergio > > > --=20 Jo=E3o Henriques --e89a8f83ab7d8f491d04b9f172a1 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Sergio,

Post the error please (tail the output file= and post it here). And yes, of course G03 supports solvation...
=
Best regards,
Joao

On Sat, Feb 25, 2012 at 3:47 PM, sergio.manzetti]~[gmail.com <owner-chemistry::ccl.net> wrote:
De= ar CCLers, I get an error message upon trying to batch a job to Gaussian 03= with solvation parameters:
=20
=20 %nproc=3D4
=20 %Mem=3D1900MB
=20 #P MPW1PW91/6-311+G(d)/auto scrf=3D(solvent=3Dwater) guess=3Dsave polar #=20 # Opt
=20 #=A0 polar
=20 # Gfinput IOP(6/7=3D3)=A0 Pop=3Dfull=A0 Density=A0 Test
=20 # Units(Ang,Deg)
=20
=20
=20 Does G03 support solvation at all?
=20
=20 All the best
=20
=20
=20 Sergio
=20
=20
=20 =A0<= /font>



--
Jo=E3o Henri= ques
--e89a8f83ab7d8f491d04b9f172a1-- From owner-chemistry@ccl.net Mon Feb 27 09:36:00 2012 From: "Mark Iron Mark.A.Iron%weizmann.ac.il" To: CCL Subject: CCL:G: Gaussian input file command Message-Id: <-46385-120227092838-18114-cttdgK7LVLv/umuG777aKA:-:server.ccl.net> X-Original-From: Mark Iron Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_8BA3C36547B54AEE9463DF03A0E550C8weizmannacil_" Date: Mon, 27 Feb 2012 14:28:25 +0000 MIME-Version: 1.0 Sent to CCL by: Mark Iron [Mark.A.Iron]|[weizmann.ac.il] --_000_8BA3C36547B54AEE9463DF03A0E550C8weizmannacil_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable One other small point: You are using mPW1PW91 - which is a hybrid functiona= l - but also request density fitting basis sets. Density fitting allows for= faster calculation of the Coulomb integrals, which is very effective in im= proving the efficiency of calculations with GGA (a.k.a. "pure") functionals= (i.e., by reducing the problem from N^4 to N^3 scaling). However, hybrid f= unctionals, buy definition include "exact" HF exchange, which is not affect= ed by the density fitting, and thus the N^4 scaling remains. Therefore, the= re is no point in using density fitting basis sets with a hybrid functional= . In addition, the "polar" keyword appears twice, although I am not sure how = Gaussian handles this problem. Hope this help, Mark. ----------------------------------------------------- Dr. Mark Iron, Computational Chemistry Unit, Department of Chemical Research Support, Kimmelman 251, Weizmann Institute of Science, Rehovot, Israel 76100. Tel: +972 8 934 6218 Fax: +972 8 934 4142 e-mail: mark.a.iron : weizmann.ac.il web: http://compchem.weizmann.ac.il/ccu/ No trees were killed in the sending of this message. However, a large number of electrons were terribly inconvenienced. On Feb. 27, 2012, at 2:42 PM, Jo=E3o Henriques joao.henriques.32353:+:gmail= .com wrote: Dear Sergio, Post the error please (tail the output file and post it here). And yes, of = course G03 supports solvation... Best regards, Joao On Sat, Feb 25, 2012 at 3:47 PM, sergio.manzetti]~[gmail.com > wrote: Dear CCLers, I get an error message upon trying to batch a job to Gaussian = 03 with solvation parameters: %nproc=3D4 %Mem=3D1900MB #P MPW1PW91/6-311+G(d)/auto scrf=3D(solvent=3Dwater) guess=3Dsave polar # # Opt # polar # Gfinput IOP(6/7=3D3) Pop=3Dfull Density Test # Units(Ang,Deg) Does G03 support solvation at all? All the best Sergio -- Jo=E3o Henriques --_000_8BA3C36547B54AEE9463DF03A0E550C8weizmannacil_ Content-Type: text/html; charset="iso-8859-1" Content-ID: <24AB68C838892E4582008924F0ECCA0D : weizmann.ac.il> Content-Transfer-Encoding: quoted-printable One other small point: You are using mPW1PW91 - which is a hybrid functiona= l - but also request density fitting basis sets. Density fitting allows for= faster calculation of the Coulomb integrals, which is very effective in im= proving the efficiency of calculations with GGA (a.k.a. "pure") functionals (i.e., by reducing the prob= lem from N^4 to N^3 scaling). However, hybrid functionals, buy definition i= nclude "exact" HF exchange, which is not affected by the density = fitting, and thus the N^4 scaling remains. Therefore, there is no point in using density fitting basis sets with a hybrid functi= onal.

In addition, the "polar" keyword appears twice, although I a= m not sure how Gaussian handles this problem.

Hope this help,

Mark.
-------= ----------------------------------------------
Dr. Mark Iron,
Computational Chemistry Unit,
Department of Chemical Research Support,
Kimmelman 251,
Weizmann Institute of Science,
Rehovot, Israel 76100.

Tel: +972 8 934 6218
Fax: +972 8 934 4142

e-mail: mark.a.iron : weizmann.= ac.il
web: http://compchem.weizma= nn.ac.il/ccu/

No trees were killed in the sending of this message.
However, a large number of electrons were terribly inconvenienced.



On Feb. 27, 2012, at 2:42 PM, Jo=E3o Henriques joao.henriques.32353:&#= 43;:gmail.com wrote:

Dear Sergio,

Post the error please (tail the output file and post it here). And yes= , of course G03 supports solvation...

Best regards,
Joao

On Sat, Feb 25, 2012 at 3:47 PM, sergio.manzetti= ]~[gmail.com <owner-ch= emistry]~[ccl.net> wrote:
De= ar CCLers, I get an error message upon trying to batch a job to Gaussian 03= with solvation parameters:

%nproc=3D4
%Mem=3D1900MB
#P MPW1PW91/6-311+G(d)/auto scrf=3D(solvent=3Dwater) guess=3Dsave polar= #
# Opt
#  polar
# Gfinput IOP(6/7=3D3)  Pop=3Dfull  Density  Test
# Units(Ang,Deg)


Does G03 support solvation at all?

All the best


Sergio


 



--
Jo=E3o Henriques

--_000_8BA3C36547B54AEE9463DF03A0E550C8weizmannacil_-- From owner-chemistry@ccl.net Mon Feb 27 10:10:00 2012 From: "sergio.manzetti:gmail.com" To: CCL Subject: CCL: HOMA index for Dibenzo[a,l]pyrene Message-Id: <-46386-120227084802-25516-g7WTb10I1FsHW3lhlCiDQQ!^!server.ccl.net> X-Original-From: sergio.manzetti*|*gmail.com Content-Type: multipart/alternative; boundary="========GMXBoundary134751330350223551510" Date: Mon, 27 Feb 2012 14:43:43 +0100 MIME-Version: 1.0 Sent to CCL by: sergio.manzetti_-_gmail.com --========GMXBoundary134751330350223551510 Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: 8bit Dear CCLrs, does anyone know where to find the HOMA index of Dibenzo[a,l]pyrene? Portella and co. have done a lot of work on this, but I wasn't able to find these values for this molecule in their studies. Thanks Sergio --========GMXBoundary134751330350223551510 Content-Type: text/html; charset="utf-8" Content-Transfer-Encoding: quoted-printable Dear CCL= rs, does anyone know where to find the HOMA index of Dibenzo[a,l]pyrene? Po= rtella and co. have done a lot of work on this, but I wasn't able to find t= hese values for this molecule in their studies.
=20
=20 Thanks
=20
=20 Sergio
=20

=20 =C2=A0

=20
=20   --========GMXBoundary134751330350223551510-- From owner-chemistry@ccl.net Mon Feb 27 13:27:01 2012 From: "Fabio Coelho fabioamsc#ig.com.br" To: CCL Subject: CCL: Calulate RMSD Message-Id: <-46387-120227132541-6023-Qi9LyZYiMyWKxDy1JdWCNg_._server.ccl.net> X-Original-From: "Fabio Coelho" Date: Mon, 27 Feb 2012 13:25:39 -0500 Sent to CCL by: "Fabio Coelho" [fabioamsc- -ig.com.br] Hi all, I would like to know if there are some programs (free) that calculate the RMSD to docked ligands and the crystallographic. Berst regards Fbio From owner-chemistry@ccl.net Mon Feb 27 14:20:00 2012 From: "Prashant Kumar prashantkbio ~~ gmail.com" To: CCL Subject: CCL: Calulate RMSD Message-Id: <-46388-120227141823-8243-EsNfr6an51/cN72tvjlIVA__server.ccl.net> X-Original-From: Prashant Kumar Content-Type: multipart/alternative; boundary=0015175df040ecad8d04b9f6f8c2 Date: Mon, 27 Feb 2012 20:17:56 +0100 MIME-Version: 1.0 Sent to CCL by: Prashant Kumar [prashantkbio_._gmail.com] --0015175df040ecad8d04b9f6f8c2 Content-Type: text/plain; charset=ISO-8859-1 Hello, Use chimera. Best P. On Mon, Feb 27, 2012 at 7:25 PM, Fabio Coelho fabioamsc#ig.com.br < owner-chemistry|a|ccl.net> wrote: > > Sent to CCL by: "Fabio Coelho" [fabioamsc- -ig.com.br] > Hi all, > > I would like to know if there are some programs (free) that calculate the > RMSD to docked ligands and the crystallographic. > > Berst regards > Fbio> > > --0015175df040ecad8d04b9f6f8c2 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hello,

Use chimera.

Best
<= div>
P.

On Mon, Feb 27= , 2012 at 7:25 PM, Fabio Coelho fabioamsc#ig.c= om.br <= owner-chemistry|a|ccl.net> wrote:

Sent to CCL by: "Fabio =A0Coelho" [fabioamsc- -ig.com.br]
Hi all,

I would like to know if there are some programs (free) that calculate the R= MSD to docked ligands and the crystallographic.

Berst regards
Fbio



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--0015175df040ecad8d04b9f6f8c2-- From owner-chemistry@ccl.net Mon Feb 27 15:52:00 2012 From: "Sean Ekins ekinssean(_)yahoo.com" To: CCL Subject: CCL: Call for users: Open Drug Discovery Teams (ODDT) app Message-Id: <-46389-120227152307-19819-VuoLzDvpiTG3C5WXY7inMQ]_[server.ccl.net> X-Original-From: "Sean Ekins" Date: Mon, 27 Feb 2012 15:23:05 -0500 Sent to CCL by: "Sean Ekins" [ekinssean{:}yahoo.com] The Open Drug Discovery Teams (ODDT) project is a mobile app primarily intended as a research topic aggregator of open science data integrated from various sources on the internet. It exists to facilitate interdisciplinary teamwork and to relieve the user from data overload. Initial research topics include areas of chemistry and adjacent molecule-oriented biomedical sciences, with an emphasis on those which are most amenable to open research at present. The ODDT project uses a free mobile app for iOS-based devices (iPhone, iPod and iPad) as the hub. The app has a Flipboard-inspired interface, and serverside infrastructure for hosting data and value added services. The project is open to participation from anyone, and much of the content is derived from public sources but is amenable to commercial data input. We would like to announce that an alpha version of this app is available for users to access upon request from us for non-commercial uses and under no warranty. We invite anyone who is interested in participating in the alpha evaluation program, and providing constructive feedback, to contact either myself or Alex: Dr. Sean Ekins Collaborations in Chemistry, A division of Collaborations in Communications, Inc. ekinssean{=}yahoo.com Dr. Alex M. Clark Molecular Materials Informatics, Inc. aclark{=}molmatinf.com For more information, see: http://www.scimobileapps.com/index.php?title=Open_Drug_Discovery_Teams http://collabchem.com http://cheminf20.org From owner-chemistry@ccl.net Mon Feb 27 16:26:00 2012 From: "Symon Gathiaka sgathiaka#,#gmail.com" To: CCL Subject: CCL: Calulate RMSD Message-Id: <-46390-120227154910-12812-h+Qq0spj//HnsoJ5P2AkOQ---server.ccl.net> X-Original-From: Symon Gathiaka Content-Type: multipart/alternative; boundary=f46d044287be9fbd8504b9f83d09 Date: Mon, 27 Feb 2012 14:49:03 -0600 MIME-Version: 1.0 Sent to CCL by: Symon Gathiaka [sgathiaka\a/gmail.com] --f46d044287be9fbd8504b9f83d09 Content-Type: text/plain; charset=ISO-8859-1 Hi, Chimera or Swiss-PdbViewer can do exactly that! Best, S On Mon, Feb 27, 2012 at 1:17 PM, Prashant Kumar prashantkbio ~~ gmail.com < owner-chemistry%x%ccl.net> wrote: > Hello, > > Use chimera. > > Best > > P. > > On Mon, Feb 27, 2012 at 7:25 PM, Fabio Coelho fabioamsc#ig.com.br < > owner-chemistry*|*ccl.net> wrote: > >> >> Sent to CCL by: "Fabio Coelho" [fabioamsc- -ig.com.br] >> Hi all, >> >> I would like to know if there are some programs (free) that calculate the >> RMSD to docked ligands and the crystallographic. >> >> Berst regards >> Fbio** >> E-mail to subscribers: CHEMISTRY*|*ccl.net or use:>> >> E-mail to administrators: CHEMISTRY-REQUEST*|*ccl.net or use>> **>> >> >> > -- ** *As is a tale, so is life: not how long it is, but how good it is, is what matters.* ** ** ** ** --f46d044287be9fbd8504b9f83d09 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hi,
=A0
Chimera or Swiss-PdbViewer can=A0do exactly that!
=A0
Best,
S

On Mon, Feb 27, 2012 at 1:17 PM, Prashant Kumar = prashantkbio ~~ gmail.com <owner-chemistry%x%ccl.net> wrote:
Hello,=20

Use chimera.

Best

P.

On Mon, Feb 27, 2012 at 7:25 PM, Fabio Coelho fabioamsc#<= a href=3D"http://ig.com.br/" target=3D"_blank">ig.com.br <ow= ner-chemistry*|*ccl.net> wrote:

Sent to CCL by: "Fabio =A0Coelho" [fabioams= c- -ig.com.br]
Hi al= l,

I would like to know if there are some programs (free) that calcu= late the RMSD to docked ligands and the crystallographic.

Berst regards
Fbio



-=3D This is automatically added t= o each message by the mailing script =3D-
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--
=A0As is a tale, so is life: not how long it is, = but how good it is, is what matters.
=A0
=A0
=A0
=A0

=A0
=A0

--f46d044287be9fbd8504b9f83d09-- From owner-chemistry@ccl.net Mon Feb 27 17:01:01 2012 From: "Andrew Orry andy..molsoft.com" To: CCL Subject: CCL: Calulate RMSD Message-Id: <-46391-120227160617-25914-9sDBf4KiJxejLsXjyV8+gA__server.ccl.net> X-Original-From: Andrew Orry Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 27 Feb 2012 13:10:30 -0800 MIME-Version: 1.0 Sent to CCL by: Andrew Orry [andy===molsoft.com] You can calculate RMSD between two ligands in MolSoft's ICM-Browser which is free. 1. Download ICM-Browser here: http://www.molsoft.com/icm_browser.html 2. Load the crystal structure and docked complex (File/Open) 3. Use the Srmsd command http://www.molsoft.com/man/icm-functions.html#Srmsd Thanks, Andrew MolSoft LLC Senior Research Scientist 11199 Sorrento Valley Road, S209 San Diego CA 92121 Tel: 858-625-2000 x108 Fax: 828-625-2888 www.molsoft.com www.twitter.com/molsoft On 2/27/2012 10:25 AM, Fabio Coelho fabioamsc#ig.com.br wrote: > Sent to CCL by: "Fabio Coelho" [fabioamsc- -ig.com.br] > Hi all, > > I would like to know if there are some programs (free) that calculate the RMSD to docked ligands and the crystallographic. > > Berst regards > Fbio> -- Andrew Orry Ph.D. MolSoft LLC Senior Research Scientist 11199 Sorrento Valley Road, S209 San Diego CA 92121 Tel: 858-625-2000 x108 Fax: 828-625-2888 www.molsoft.com From owner-chemistry@ccl.net Mon Feb 27 17:36:00 2012 From: "Kyle Lutz kyle.r.lutz[a]gmail.com" To: CCL Subject: CCL: Calulate RMSD Message-Id: <-46392-120227163026-8051-2hN+iiEd4GnvCWxcB9BfBQ-.-server.ccl.net> X-Original-From: Kyle Lutz Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 27 Feb 2012 16:30:17 -0500 MIME-Version: 1.0 Sent to CCL by: Kyle Lutz [kyle.r.lutz:-:gmail.com] >> Sent to CCL by: "Fabio  Coelho" [fabioamsc- -ig.com.br] >> Hi all, >> >> I would like to know if there are some programs (free) that calculate the >> RMSD to docked ligands and the crystallographic. Hi Fabio, The open-source chemkit library can calculate the RMSD between two molecules. See the rmsd() method of the MoleculeAligner class (http://doc.chemkit.org/api/classchemkit_1_1_molecule_aligner.html). Let me know if you have any questions or would like to see some example code. Cheers, Kyle From owner-chemistry@ccl.net Mon Feb 27 18:29:00 2012 From: "Abhik Seal abhik1368/./gmail.com" To: CCL Subject: CCL: Calulate RMSD Message-Id: <-46393-120227182348-21885-wkALTZx1620obpeaWUDH8Q]=[server.ccl.net> X-Original-From: Abhik Seal Content-Type: multipart/alternative; boundary=e89a8f234a318bd4d704b9fa6624 Date: Mon, 27 Feb 2012 18:23:20 -0500 MIME-Version: 1.0 Sent to CCL by: Abhik Seal [abhik1368|*|gmail.com] --e89a8f234a318bd4d704b9fa6624 Content-Type: text/plain; charset=ISO-8859-1 Dear Sir, Does molsoft measures two protein Structure rmsd ? Abhik Seal Indiana University Bloomington Department of Chemical Informatics abseal#,#indiana.edu *OSDD CHEMINFORMATICS* +18123699097 http://mypage.iu.edu/~abseal/index.htm On Mon, Feb 27, 2012 at 4:10 PM, Andrew Orry andy..molsoft.com < owner-chemistry#,#ccl.net> wrote: > > Sent to CCL by: Andrew Orry [andy===molsoft.com] > You can calculate RMSD between two ligands in MolSoft's ICM-Browser which > is free. > 1. Download ICM-Browser here: http://www.molsoft.com/icm_**browser.html > 2. Load the crystal structure and docked complex (File/Open) > 3. Use the Srmsd command http://www.molsoft.com/man/** > icm-functions.html#Srmsd > > Thanks, > Andrew > > MolSoft LLC > Senior Research Scientist > 11199 Sorrento Valley Road, S209 > San Diego > CA 92121 > Tel: 858-625-2000 x108 > Fax: 828-625-2888 > www.molsoft.com > www.twitter.com/molsoft > > > > On 2/27/2012 10:25 AM, Fabio Coelho fabioamsc#ig.com.br wrote: > >> Sent to CCL by: "Fabio Coelho" [fabioamsc- -ig.com.br] >> Hi all, >> >> I would like to know if there are some programs (free) that calculate the >> RMSD to docked ligands and the crystallographic. >> >> Berst regards >> Fbio> >> > > > -- > Andrew Orry Ph.D. > MolSoft LLC > Senior Research Scientist > 11199 Sorrento Valley Road, S209 > San Diego > CA 92121 > Tel: 858-625-2000 x108 > Fax: 828-625-2888 > www.molsoft.com> http://www.ccl.net/cgi-bin/**ccl/send_ccl_message http://www.ccl.net/cgi-bin/**ccl/send_ccl_message chemistry/announcements/**conferences/ > > Search Messages: http://www.ccl.net/chemistry/**searchccl/index.shtml http://www.ccl.net/spammers.**txt > > RTFI: http://www.ccl.net/chemistry/**aboutccl/instructions/ > > > --e89a8f234a318bd4d704b9fa6624 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Sir,

Does molsoft measures two protein Structure rm= sd ?
=A0
=A0
Abhik Seal
Indiana University Bloomington
Department of Chemical Informatics



On Mon, Feb 27, 2012 at 4:10 PM, Andrew = Orry andy..molsoft.com <owner-chemistry#,#ccl.net= > wrote:

Sent to CCL by: Andrew Orry [andy=3D=3D=3Dmolsoft.com]
You can calculate RMSD between two ligands in MolSoft's ICM-Browser whi= ch is free.
1. Download ICM-Browser here: http://www.molsoft.com/icm_browser.html=
2. Load the crystal structure and docked complex (File/Open)
3. Use the Srmsd command http://www.molsoft.com/man/icm-funct= ions.html#Srmsd

Thanks,
Andrew

MolSoft LLC
Senior Research Scientist
11199 Sorrento Valley Road, S209
San Diego
CA 92121
Tel: 858-625-2000 x108
Fax: = 828-625-2888
www.molsoft.com www.twitter.co= m/molsoft



On 2/27/2012 10:25 AM, Fabio Coelho fabioamsc#ig.com.br wrote:
Sent to CCL by: "Fabio =A0Coelho" [fabioamsc- -ig.com.br]
Hi all,

I would like to know if there are some programs (free) that calculate the R= MSD to docked ligands and the crystallographic.

Berst regards
Fbio>


--
Andrew Orry Ph.D.
MolSoft LLC
Senior Research Scientist
11199 Sorrento Valley Road, S209
San Diego
CA 92121
Tel: 858-625-2000 x108
Fax: = 828-625-2888
www.molsoft.com


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--e89a8f234a318bd4d704b9fa6624--