From owner-chemistry@ccl.net Wed Mar 10 00:32:01 2010 From: "Prasenjit SEAL prasenjit.seal|,|crm2.uhp-nancy.fr" To: CCL Subject: CCL:G: Isotope Message-Id: <-41407-100309125920-28148-8P6nObCXv/bTxqoOoS+H7g:-:server.ccl.net> X-Original-From: Prasenjit SEAL Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 09 Mar 2010 18:59:05 +0100 MIME-Version: 1.0 Sent to CCL by: Prasenjit SEAL [prasenjit.seal##crm2.uhp-nancy.fr] Hi CCL subscribers, Can anybody tell me which software can perform optimization of isotopes? I want to perform a geometry optimization of D2 and HD molecules. If it is Gaussian or MOLPRO, then how I should proceed? Thanks in advance. Cheers, PS From owner-chemistry@ccl.net Wed Mar 10 02:52:01 2010 From: "Marek Maly marek.maly|-|ujep.cz" To: CCL Subject: CCL: MMPBSA in case of highly water accessible molecules ? Message-Id: <-41408-100310023731-21315-FODmIU5Hak10QmcKSfHBig]![server.ccl.net> X-Original-From: "Marek Maly" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-2; format=flowed; delsp=yes Date: Wed, 10 Mar 2010 08:33:07 +0100 MIME-Version: 1.0 Sent to CCL by: "Marek Maly" [marek.maly[A]ujep.cz] Dear all, I am just curious if the commonly used and for example in Amber MM/PBSA implementation highly recommended value 1 for dielectric constant of the solut (in Amber it is parameter INDI) is ideal also in case of MM/PBSA calculations of free energy of binding of two molecules which interior is pretty accessible to water molecules. I am asking because I have experienced some small positive values of dG (4.91, 2.48) in case of nicely complexated singlestrand DNA and small dendrimer which interior is almost fully accessible for water molecules. Although dH was negative in agreement with evident complexation, positive entropic penalty -TdS more than compensated enthalpic gain. I tried to increase solute diel. constant (INDI = 2,3 - 7) and I got nice improvement (more negative values dH) with saturation of dH around INDI = 6. But of course I would like to prevent me from the experiments which might be in contradiction with theory. In this case would be for me better to stay with INDI=1 and explain small positive values of dG as the result of inaccuracy of the methodology (especially in case of normal mode analysis) I have to say that I tried both, single and three trajectory approach with the similar behaviour. I think that my statistic is pretty good (analyses (including entropy) of 400 frames from the last 4ns of 14ns simulation ). Thanks in advance for any helpful information/advice ! Best wishes, Marek -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/ From owner-chemistry@ccl.net Wed Mar 10 04:27:00 2010 From: "Serdar Bado?lu sbadoglu+/-gazi.edu.tr" To: CCL Subject: CCL:G: Isotope Message-Id: <-41409-100310041830-23399-t3IGrCKg+XynCBZxeaGyeQ-.-server.ccl.net> X-Original-From: "Serdar Bado?lu" Date: Wed, 10 Mar 2010 09:18:13 -0000 Sent to CCL by: "Serdar Bado?lu" [sbadoglu_-_gazi.edu.tr] Something like that should work in Gaussian: %chk=h2-opt-freq.chk %mem=1GB %nproc=1 # opt freq b3lyp/6-311+g(d) geom=connectivity Title Card Required 0 1 H H(Iso=2) 1 B1 B1 0.74000000 1 2 1.0 2 Here, the main point you ask is the definition of isotopes. In the z-matrix section just add (Iso=N) command for the corresponding atom, then it will be handled as the isotope. Above input text shows HD molecule, hydrogen #1 defined as hydrogen, hydrogen #2 defined as deuterium. Hope this helps. > > Sent to CCL by: Prasenjit SEAL [prasenjit.seal##crm2.uhp-nancy.fr] > Hi CCL subscribers, > > Can anybody tell me which software can perform optimization of isotopes? > I want to perform a geometry optimization of D2 and HD molecules. > > If it is Gaussian or MOLPRO, then how I should proceed? > > Thanks in advance. > > Cheers, > PS > -- Serdar BADOGLU http://docs.google.com/View?id=dckx8v2c_29g9scr9fv From owner-chemistry@ccl.net Wed Mar 10 09:44:00 2010 From: "Praveen Kumar Shrivastava praveenshrivastav###gmail.com" To: CCL Subject: CCL: thesis Message-Id: <-41410-100309205634-1145-bH8HZ1RoIm8ada2m5WEuvA##server.ccl.net> X-Original-From: Praveen Kumar Shrivastava Content-Type: multipart/alternative; boundary=00163630eda947f63f0481671b4d Date: Wed, 10 Mar 2010 05:39:06 +0530 MIME-Version: 1.0 Sent to CCL by: Praveen Kumar Shrivastava [praveenshrivastav]-[gmail.com] --00163630eda947f63f0481671b4d Content-Type: text/plain; charset=ISO-8859-1 Dear Ellen Consult The Cambridge Structural Database - The world repository of small molecule crystal structures www.ccdc.cam.ac.uk/products/csd/ Know about database en.wikipedia.org/wiki/*Cambridge*_Structural_*Database* I hope this will solve your problem. With my best wishes Praveen On Tue, Mar 9, 2010 at 3:23 PM, Ellen Peeters ellen.peeters.. student.uhasselt.be wrote: > > Sent to CCL by: "Ellen Peeters" [ellen.peeters,+,student.uhasselt.be] > Hello > My name is Ellen Peeters, and i'm studying chemistry at the University > Hasselt in Belgium. For this > third year i have to make some kind of thesis where i do some computational > work. For this work i > have to find the coordinates and other crystallographic data about > Vanadiumcomplexes like > oxoperoxocitratovanadates, dioxocitratovanadates and peroxomalatovanadates. > Maybe somebody > knows where i can find this information? > > With kind regards > Ellen Peeters > ellen.peeters|a|student.uhasselt.be> > > --00163630eda947f63f0481671b4d Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

Dear Ellen

=A0

Consult=A0The Cambridg= e Structural Database - The world repository of small molecule crystal struct= ures

www.ccdc.cam.ac.uk/products/csd/

=A0

Know about database=A0=

en.wikipedia.org/wiki/Cambridge_Structural_<= b>Database=A0

=A0

I hope this will solve= your problem.

=A0

With my best wishes

Praveen

On Tue, Mar 9, 2010 at 3:23 PM, Ellen Pee= ters ellen.peeters..student.uhasselt= .be <ow= ner-chemistry,ccl.net> wrote:

Sent to CCL by: "Ellen =A0Peeters" [ellen.peeters,+,student.uhasselt.be]
Hello
My name is Ellen Peeters, and i'm studying chemistry at the University = Hasselt in Belgium. For this
third year i have to make some kind of thesis where i do some computational= work. For this work i
have to find the coordinates and other crystallographic data about Vanadium= complexes like
oxoperoxocitratovanadates, dioxocitratovanadates and peroxomalatovanadates.= Maybe somebody
knows where i can find this information?

With kind regards
Ellen Peeters
ellen.peeters|a|st= udent.uhasselt.be

--00163630eda947f63f0481671b4d-- From owner-chemistry@ccl.net Wed Mar 10 13:07:01 2010 From: "Jamin Krinsky jamink(a)berkeley.edu" To: CCL Subject: CCL:G: Isotope Message-Id: <-41411-100310130538-27378-4skGL+qcXTiWB/6PPj0oCw%a%server.ccl.net> X-Original-From: Jamin Krinsky Content-Type: multipart/alternative; boundary=0016362842429aeccd048176246e Date: Wed, 10 Mar 2010 10:05:27 -0800 MIME-Version: 1.0 Sent to CCL by: Jamin Krinsky [jamink,+,berkeley.edu] --0016362842429aeccd048176246e Content-Type: text/plain; charset=ISO-8859-1 Hi Prasenjit, In a normal ab initio calculation (DFT, etc.) you are assuming the Born-Oppenheimer approximation that the nuclei are not moving, so you are going to get the same geometry for H and D substitution. What will change with isotope are frequency-dependent properties: zero point energies, etc. The reason why X-D bonds are shorter than X-H bonds is that the lowest vibrational level of X-D is lower than that for X-H, so it sits closer two the equilibrium geometry at the BOTTOM of an anharmonic potential well. I think you'd have to solve a frequency-coupled nuclear Schrodinger equation to get that behavior in a geometry optimization. Please someone correct me if I'm wrong. Regards, Jamin On Tue, Mar 9, 2010 at 9:59 AM, Prasenjit SEAL prasenjit.seal|,| crm2.uhp-nancy.fr wrote: > > Sent to CCL by: Prasenjit SEAL [prasenjit.seal##crm2.uhp-nancy.fr] > Hi CCL subscribers, > > Can anybody tell me which software can perform optimization of isotopes? I > want to perform a geometry optimization of D2 and HD molecules. > > If it is Gaussian or MOLPRO, then how I should proceed? > > Thanks in advance. > > Cheers, > PShttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > -- Jamin L Krinsky, Ph.D. Molecular Graphics and Computation Facility 175 Tan Hall, University of California, Berkeley, CA 94720 jamink-*-berkeley.edu, 510-643-0616 http://glab.cchem.berkeley.edu --0016362842429aeccd048176246e Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Prasenjit,
In a normal ab initio calculation (DFT, etc.) you are assu= ming the Born-Oppenheimer approximation that the nuclei are not moving, so = you are going to get the same geometry for H and D substitution. What will = change with isotope are frequency-dependent properties: zero point energies= , etc. The reason why X-D bonds are shorter than X-H bonds is that the lowe= st vibrational level of X-D is lower than that for X-H, so it sits closer t= wo the equilibrium geometry at the BOTTOM of an anharmonic potential well. = I think you'd have to solve a frequency-coupled nuclear Schrodinger equ= ation to get that behavior in a geometry optimization. Please someone corre= ct me if I'm wrong.
Regards,
Jamin


On Tue, Mar 9, 2010= at 9:59 AM, Prasenjit SEAL prasenjit.seal|,|crm2.uhp-nancy.fr <owner-chemistry-*-ccl.net> wrote:

Sent to CCL by: Prasenjit SEAL [prasenjit.seal##crm2.uhp-nancy.fr]
Hi CCL subscribers,

Can anybody tell me which software can perform optimization of isotopes? I = want to perform a geometry optimization of D2 and HD molecules.

If it is Gaussian or MOLPRO, then how I should proceed?

Thanks in advance.

Cheers,
PS



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--
Jamin L Krinsky, Ph.D.<= br>Molecular Graphics and Computation Facility
175 Tan Hall, University = of California, Berkeley, CA 94720
jamink-*-berkeley.edu, 510-643-0616
http://glab.cchem.berkeley.edu

--0016362842429aeccd048176246e-- From owner-chemistry@ccl.net Wed Mar 10 13:41:01 2010 From: "partha pratim kundu partha1kundu_+_gmail.com" To: CCL Subject: CCL: installation of GAR2PED software Message-Id: <-41412-100309104603-20599-LZX5rjU6WeuiJitTQimYNQ^^^server.ccl.net> X-Original-From: "partha pratim kundu" Date: Tue, 9 Mar 2010 10:45:59 -0500 Sent to CCL by: "partha pratim kundu" [partha1kundu++gmail.com] Dear All, Can anybody help me in installing GAR2PED software. I am new in linux. So please write all the commands beginning from compressing the tar.z file. Thanks in advance. Partha. From owner-chemistry@ccl.net Wed Mar 10 14:16:01 2010 From: "partha pratim kundu partha1kundu*yahoo.com" To: CCL Subject: CCL: GAR2PED installation Message-Id: <-41413-100310135343-22881-xGmpTdEeG+B0NvTg9kF44g-#-server.ccl.net> X-Original-From: "partha pratim kundu" Date: Wed, 10 Mar 2010 13:53:39 -0500 Sent to CCL by: "partha pratim kundu" [partha1kundu~~yahoo.com] Dear All, Please help me in installing the GAR2PED program. I am new in linux so please send the commands beginning from untaring the tar.z file. Thanks in advance. Partha. partha1kundu_._yahoo.com From owner-chemistry@ccl.net Wed Mar 10 16:01:00 2010 From: "rafapa[]us.es" To: CCL Subject: CCL: installation of GAR2PED software Message-Id: <-41414-100310152849-22121-LcH2UfeSkpQHojA3zoxV8w..server.ccl.net> X-Original-From: Content-Disposition: inline Content-Language: es Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=iso-8859-1 Date: Wed, 10 Mar 2010 20:28:34 +0100 MIME-Version: 1.0 Sent to CCL by: [rafapa.(_).us.es] Dear Partha=2C unfortunately it=27s not that easy=2E I could try to help but I need to = know which fortran compiler and Linux distribution are you using=2E Last time I tried (Oct 2009) I needed to change a couple of lines in som= e of the fortran files=2E Best regards=2C Rafael R=2E Pappalardo Univ=2E de Sevilla (Spain) ----- Mensaje original ----- De=3A =22partha pratim kundu partha1kundu=5F+=5Fgmail=2Ecom=22 =3Cowner-= chemistry=40ccl=2Enet=3E Fecha=3A Mi=E9rcoles=2C Marzo 10=2C 2010 8=3A07 pm Asunto=3A CCL=3A installation of GAR2PED software A=3A =22Pappalardo=2C Rafael R=2E -id=2342m-=22 =3Crafapa=40catedrax=2Eu= s=2Ees=3E =3E Sent to CCL by=3A =22partha pratim kundu=22 =5Bpartha1kundu++gmail=2E= com=5D =3E Dear All=2C =3E Can anybody help me in installing GAR2PED software=2E I am new in li= nux=2E = =3E So please write all the commands beginning from compressing the tar=2E= z = =3E file=2E =3E Thanks in advance=2E =3E Partha=2E =3E = =3E = =3E = =3E -=3D This is automatically added to each message by the mailing scri= pt =3D- =3E To recover the email address of the author of the message=2C please = change =3E the strange characters on the top line to the =40 sign=2E You can al= so =3E look up the X-Original-From=3A line in the mail header=2E =3E = =3E E-mail to subscribers=3A CHEMISTRY=40ccl=2Enet or use=3A =3E = =3E = =3E E-mail to administrators=3A CHEMISTRY-REQUEST=40ccl=2Enet or use =3E = =3E = =3E Subscribe/Unsubscribe=3A = =3E = =3E = =3E Before posting=2C check wait time at=3A = =3E = =3E Job=3A = =3E Conferences=3A = =3E = =3E Search Messages=3A = =3E = =3E If your mail bounces from CCL with 5=2E7=2E1 error=2C check=3A =3E = =3E = =3E RTFI=3A = =3E = =3E