From owner-chemistry@ccl.net Wed Feb 1 03:41:00 2006 From: "Konrad Hinsen khinsen*_*cea.fr" To: CCL Subject: CCL: software or online server to predict protein flexibility Message-Id: <-30734-060201022926-20715-b5YGQwyATRvUnqjGzXRnkQ,,server.ccl.net> X-Original-From: "Konrad Hinsen" Sent to CCL by: "Konrad Hinsen" [khinsen__cea.fr] On 01.02.2006, at 05:08, Eric Hu yhu_2003*|*yahoo.com wrote: > Hi, I wonder if any service exists to predict what part of a given protein is likely to be > flexible or inducible upon binding with other proteins. Thanks. Try Webnm:+:: http://www.bioinfo.no/tools/normalmodes -- ------------------------------------------------------------------------------- Konrad Hinsen Laboratoire Leon Brillouin (CEA-CNRS), CEA Saclay, 91191 Gif-sur-Yvette Cedex, France Tel.: +33-1 69 08 79 25 Fax: +33-1 69 08 82 61 E-Mail: khinsen:+:cea.fr ------------------------------------------------------------------------------- From owner-chemistry@ccl.net Wed Feb 1 04:46:00 2006 From: "D.BIO- Gerard Pujadas gerard.pujadas(_)urv.net" To: CCL Subject: CCL: software or online server to predict protein flexibility Message-Id: <-30735-060201032646-25544-tNhtP8lFy+gZ2nGWmXSn7g||server.ccl.net> X-Original-From: "D.BIO- Gerard Pujadas" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" ; format="flowed" Date: Wed, 1 Feb 2006 08:27:48 +0100 Mime-Version: 1.0 Sent to CCL by: "D.BIO- Gerard Pujadas" [gerard.pujadas#urv.net] Dear Eric, > >Hi, I wonder if any service exists to predict >what part of a given protein is likely to be >flexible or inducible upon binding with other >proteins. Thanks. > try Flexweb (http://flexweb.asu.edu/) for the analysis of flexibility in biomolecules Gerard -- ======================== NOTE: NEW ADDRESS AND E-MAIL ======================== Dr. Gerard Pujadas Grup de recerca en "Vi i Salut" Dept. Bioquímica i Biotecnologia room 106 Campus de Sant Pere Sescelades e-mail: gerard.pujadas,,urv.net Univ. Rovira i Virgili phone: 34-977 559565 C/ Marcel·lí Domingo fax: 34-977 559597 43007 Tarragona (CATALONIA) State: Spain (European Union) =========================================================================== From owner-chemistry@ccl.net Wed Feb 1 08:51:00 2006 From: "john furr john.furr|*|gmail.com" To: CCL Subject: CCL: Dynamol Update Message-Id: <-30736-060201072103-25423-K9vlARa+PT9Ybv2tCndjLA,server.ccl.net> X-Original-From: john furr Content-Type: multipart/alternative; boundary="----=_Part_16805_5030751.1138796456094" Date: Wed, 1 Feb 2006 07:20:56 -0500 MIME-Version: 1.0 Sent to CCL by: john furr [john.furr]_[gmail.com] ------=_Part_16805_5030751.1138796456094 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Peter, Dynamol should run an any modern Linux distribution. I believe you will need at least a 2.4.X kernel. The download folders are for the build platforms. I recommend trying the Fedora_Core4 version first as it is uses gcc 4.0 which provides some performance gains. Please drop me a line at john.furr=gmail.com and let me know if you get it installed. Cheers John Furr Dynamol Inc. http://www.dynamol.com john.furr=gmail.com On 1/31/06, Peter Gannett pgannett^hsc.wvu.edu wrote: > > Sent to CCL by: "Peter Gannett" [pgannett[a]hsc.wvu.edu] > This is a MIME message. If you are reading this text, you may want to > consider changing to a mail reader or gateway that understands how to > properly handle MIME multipart messages. > > --=3D__Part35179BED.0__=3D > Content-Type: text/plain; charset=3DUS-ASCII > Content-Transfer-Encoding: 7bit > > Will this installation work on a Redhat flavor of linux? The gz file > says fedora. Thanks. > > Pete > > >>> owner-chemistry*ccl.net 01/25/06 1:39 PM >>> > > Sent to CCL by: john furr [john.furr__gmail.com] > ------=3D_Part_837_9052651.1138205595542 > Content-Type: text/plain; charset=3DISO-8859-1 > Content-Transfer-Encoding: quoted-printable > Content-Disposition: inline > > It has been brought to my attention that I have not included install > instructions for the Linux versions of Dynamol. > > For those that are interested: > > right click on the download link and choose save as: > > gunzip dynamol-install.gz > chmod +x dynamol-install > ./dynamol-intstall > > **Note the archive is self installing and it is important to preserve > the > exact name "dynamol-install" Run the last step as root to install > system > wide...or as a normal user for a local install. > > Cheers > > John Furr > Dynamol Inc. > http://www.dynamol.com > john.furr*_*gmail.com > > ------=3D_Part_837_9052651.1138205595542 > Content-Type: text/html; charset=3DISO-8859-1 > Content-Transfer-Encoding: quoted-printable > Content-Disposition: inline > > It has been brought to my attention that I have not included install > instru=3D > ctions for the Linux versions of Dynamol. 
>
> For those that are interested:
>
> right click on the download link and choose save as:
>
> gunzip dynamol-install.gz
> chmod +x dynamol-install
> ./dynamol-intstall
>
> **Note the archive is self installing and it is important to preserve > the exact name "dynamol-install"  Run the last step as > root =3D > to > install system wide...or as a normal user for a local install.
>
> Cheers
>
> John Furr
> Dynamol Inc.
> href=3D"http://www.dynamol.comhttp://www.dynamol.com
> john.furr*_*gmail.com
> > ------=3D_Part_837_9052651.1138205595542--http://www.ccl.net/chemist= ry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--=3D__Part35179BED.0__=3D > Content-Type: text/html; charset=3DISO-8859-1 > Content-Transfer-Encoding: quoted-printable > Content-Description: HTML > > > charset=3D3Diso-8859-1"=3D > > > > >
Will this installation work on a Redhat flavor of linux?  The g= z > =3D > file says fedora.  Thanks.
>
 
>
Pete

>>> owner-chemistry*ccl.net 01/25/06 1:39 PM = =3D > >>>
>
Sent to CCL by: john furr [ > john.furr__gmail.c=3D > om]
------=3D3D_Part_837_9052651.1138205595542
Content-Type: > text/plain=3D > ; charset=3D3DISO-8859-1
Content-Transfer-Encoding: > quoted-printable
Co=3D > ntent-Disposition: inline

It has been brought to my attention that > =3D > I have not included install
instructions for the Linux versions of =3D > Dynamol.

For those that are interested:

right click on the = =3D > download link and choose save as:

gunzip dynamol-install.gz >
chmod=3D > +x dynamol-install
./dynamol-intstall

**Note the archive is =3D > self installing and it is important to preserve the
exact name =3D > "dynamol-install"  Run the last step as root to install > system
wide=3D > ..or as a normal user for a local install.

Cheers

John =3D > Furr
Dynamol Inc.
> http://www.dynam=3D > ol.com
john.furr*_*gmail.com >

------=3D3D_Part_837_9052651.11382=3D > 05595542
Content-Type: text/html; > charset=3D3DISO-8859-1
Content-Transf=3D > er-Encoding: quoted-printable
Content-Disposition: inline

It ha= s > =3D > been brought to my attention that I have not included install > instru=3D3D
=3D > ctions for the Linux versions of Dynamol.&nbsp; > <br>
<br>=3D > ;
For those that are interested:<br>
<br>
right clic= k > =3D > on the download link and choose save as:<br>
<br>
gunzi= p > =3D > dynamol-install.gz<br>
chmod +x > dynamol-install<br>
./dyn=3D > amol-intstall<br>
<br>
**Note the archive is self =3D > installing and it is important to preserve
the exact name > &quot;dyna=3D > mol-install&quot;&nbsp; Run the last step as root > =3D3D
to
inst=3D > all system wide...or as a normal user for a local > install.<br>
<=3D > ;br>
Cheers<br>
<br>
John > Furr<br>
Dynamol=3D > Inc.<br>
<a href=3D3D3D" ?>http://www.dynamol.com"> http=3D > ://www.dynamol.com</a><br>
<a href=3D3D3D" href=3D3D"ma=3D > ilto:john.furr*_*gmail.com" ?>mailto:john.furr*_*gmail.com > ">john.fur=3D > r*_*gmail.com< > ;/a><br>

------=3D3D_Part_837_9052651.1138205=3D > 595542--



-=3D3D This is automatically added to each messag= e =3D > by the mailing script =3D3D-
To recover the email address of the autho= r =3D > of the message, please change
the strange characters on the top line t= o > =3D > the * sign. You can also
look up the X-Original-From: line in the mail > =3D > header.
 &n=3D > bsp;    http://www.ccl.net/cgi-bin/ccl/send_ccl_m=3D > essage">http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail > =3D > to administrators: CHEMISTRY-REQUEST*ccl.net or > use
   &n=3D > bsp;  ">http=3D > > ://www.ccl.net/cgi-bin/ccl/send_ccl_message

Subscribe/Unsubscr= ib=3D > e:
      http://www.ccl.net/chemist=3D > ry/sub_unsub.shtml">http://www.ccl.net/chemistry/sub_unsub.shtml >
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Job: > http://www.=3D > ccl.net/jobs
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Search Messages: http://www.ccl.net/htd=3D > ig ">http://www.ccl.net/htdig  (login: ccl, Password: =3D > search)
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RTFI: http://www.ccl.ne=3D > t/chemistry/aboutccl/instructions/"> > http://www.ccl.net/chemistry/aboutccl/i=3D > > nstructions/

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> > --=3D__Part35179BED.0__=3D-- > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > > ------=_Part_16805_5030751.1138796456094 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Peter,

Dynamol should run an any modern Linux distribution.  I believe you will need at least a 2.4.X kernel.  The download folders are for the build platforms.  I recommend trying the Fedora_Core4 version first as it is uses gcc 4.0 which provides some performance gains. 

Please drop me a line at john.furr=g= mail.com and let me know if you get it installed. 

Cheers
John Furr
Dynamol Inc.
http://www.dynamol.com
john.furr=gmail.com

= On 1/31/06, Peter= Gannett pgannett^hsc.wvu.edu < owner-chemistry=ccl.net> wrote:
Sent to CCL by: "Peter Gannett" [pgan= nett[a]hsc.wvu.edu]
This is a MIME message. If you are reading this text, you may want toconsider changing to a mail reader or gateway that understands how to
= properly handle MIME multipart messages.

--=3D__Part35179BED.0__=3D<= br> Content-Type: text/plain; charset=3DUS-ASCII
Content-Transfer-Encoding: = 7bit

Will this installation work on a Redhat flavor of linux? &= nbsp;The gz file
says fedora.  Thanks.

Pete

>= >> owner-chemistry* ccl.net 01/25/06 1:39 PM >>>
Sent to CCL by: john furr [john.furr__gmail.com]
------=3D_Part_837_905= 2651.1138205595542
Content-Type: text/plain; charset=3DISO-8859-1
Con= tent-Transfer-Encoding: quoted-printable
Content-Disposition: inline

It has been brought to my attention = that I have not included install
instructions for the Linux versions of = Dynamol.

For those that are interested:

right click on the do= wnload link and choose save as:

gunzip dynamol-install.gz
chmod +x dynamol-install
./dynamol-= intstall

**Note the archive is self installing and it is important t= o preserve
the
exact name "dynamol-install"  Run = the last step as root to install
system
wide...or as a normal user for a local install.

Cheers=

John Furr
Dynamol Inc.
htt= p://www.dynamol.com
john.furr*_*gmail.com

------=3D_Part_837_= 9052651.1138205595542
Content-Type: text/html; charset=3DISO-8859-1
Content-Transfer-Encod= ing: quoted-printable
Content-Disposition: inline

It has been bro= ught to my attention that I have not included install
instru=3D
ction= s for the Linux versions of Dynamol.&nbsp; <br>
<br>
For those that are interested:<br>
<br>right click on the download link and choose save as:<br>
<br&g= t;
gunzip dynamol-install.gz<br>
chmod +x dynamol-install<br= >
./dynamol-intstall<br>
<br>
**Note the archive is sel= f installing and it is important to preserve
the exact name &quot;dy= namol-install&quot;&nbsp; Run the last step as
root =3D
to install system wide...or as a normal user for a local install.<br><br>
Cheers<br>
<br>
John Furr<br>
Dyn= amol Inc.<br>
<a href=3D3D" http://www.dynamol.com"><A
href=3D"http://www.dynamol.comhttp://www.dy= namol.com</a><br>
<a href=3D3D"mailto: john.furr*_*gmail.com">john.furr*_*gmail.com</a><br>= ;

------=3D_Part_837_9052651.1138205595542--
Content-Type: text/html; charset=3DISO-8859-1
Content-Transfer-Enc= oding: quoted-printable
Content-Description: HTML

<HTML><HEAD>
<META h= ttp-equiv=3D3DContent-Type content=3D3D"text/html; charset=3D3Diso-885= 9-1"=3D
>
<META content=3D3D"MSHTML 6.00.2900.2802&qu= ot; name=3D3DGENERATOR></HEAD>
<BODY style=3D3D"MARGIN: 4px 4px 1px; FONT: 10pt Tahoma"&g= t;
<DIV>Will this installation work on a Redhat flavor of linux?&a= mp;nbsp; The gz =3D
file says fedora.&nbsp; Thanks.</DIV>
&= lt;DIV>&nbsp;</DIV>
<DIV>Pete<BR><BR>&gt;&gt;&gt; owner-chemi= stry*ccl.net 01/25/06 1:39 PM =3D
&gt= ;&gt;&gt;<BR></DIV>
<DIV style=3D3D"COLOR: #= 000000">Sent to CCL by: john furr [ john.furr__gmail.c=3D
om]<BR>------=3D3D_Part_837_9052651.11382055= 95542<BR>Content-Type: text/plain=3D
; charset=3D3DISO-8859-1<B= R>Content-Transfer-Encoding: quoted-printable<BR>Co=3D
ntent-Di= sposition: inline<BR><BR>It has been brought to my attention th= at =3D
I have not included install<BR>instructions for the Linux version= s of =3D
Dynamol.<BR><BR>For those that are interested:<B= R><BR>right click on the =3D
download link and choose save as:&= lt;BR><BR>gunzip=20 dynamol-install.gz<BR>chmod=3D
+x dynamol-install<BR>./dyna= mol-intstall<BR><BR>**Note the archive is =3D
self installin= g and it is important to preserve the<BR>exact name =3D
"dyna= mol-install"&nbsp; Run the last step as root to install system<= BR>wide=3D
..or as a normal user for a local install.<BR><BR>Cheers<= ;BR><BR>John =3D
Furr<BR>Dynamol Inc.<BR><A href= =3D3D"http://www.dynamol.com&qu= ot;> http://www.dynam=3D
ol.com</A><BR>john.furr*_*gmail.com<BR><= BR>------=3D3D_Part_837_9052651.11382=3D
05595542<BR>Content-Ty= pe: text/html; charset=3D3DISO-8859-1<BR>Content-Transf=3D
er-Encoding: quoted-printable<BR>Content-Disposition: inline<B= R><BR>It has =3D
been brought to my attention that I have not i= ncluded install instru=3D3D<BR>=3D
ctions for the Linux versions o= f Dynamol.&amp;nbsp; &lt;br&gt;<BR>&lt;br&gt=3D
;<BR>For those that are interested:&lt;br&gt;<BR>&a= mp;lt;br&gt;<BR>right click =3D
on the download link and choos= e save as:&lt;br&gt;<BR>&lt;br&gt;<BR>gunzip = =3D
dynamol-install.gz&lt;br&gt;<BR>chmod +x dynamol-install&= amp;lt;br&gt;<BR>./dyn=3D
amol-intstall&lt;br&gt;<B= R>&lt;br&gt;<BR>**Note the archive is self =3D
installi= ng and it is important to preserve<BR>the exact name &amp;quot;dy= na=3D
mol-install&amp;quot;&amp;nbsp; Run the last step as root =3D3D= <BR>to<BR>inst=3D
all system wide...or as a normal user for = a local install.&lt;br&gt;<BR>&lt=3D
;br&gt;<BR= >Cheers&lt;br&gt;<BR>&lt;br&gt;<BR>John Furr= &lt;br&gt;<BR>Dynamol=3D
Inc.&lt;br&gt;<BR>&lt;a href=3D3D3D"<A href= =3D3D"http://www.dynamol.com&qu= ot; =3D
?>http://www.dynamol.com"</A>&gt;<A href=3D3D" http://www.dynamol.com</a"&g= t;http=3D
://www.dynamol.com&lt;/a</A>&gt;&lt;br&g= t;<BR>&lt;a href=3D3D3D"<A href=3D3D"ma=3D
ilto:j= ohn.furr*_*gmail.com " ?>mailto:john.furr*_*gma= il.com"</A>&gt;john.fur=3D
r*_*gmail.com&lt;/a&am= p;gt;&lt;br&gt;<BR><BR>------=3D3D_Part_837_9052651.113= 8205=3D
595542--<BR><BR><BR><BR>-=3D3D This is automati= cally added to each message =3D
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essage">http://www.ccl.net/cgi= -bin/ccl/send_ccl_message</A><BR><BR>E-mail =3D
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-=3D This is automatically added to each message by the mailing script= =3D-
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------=_Part_16805_5030751.1138796456094-- From owner-chemistry@ccl.net Wed Feb 1 09:26:01 2006 From: "tarun gupta hotbacteria .. rediffmail.com" To: CCL Subject: CCL: q.kollua in .c format Message-Id: <-30737-060201035343-2340-QbatgS/iXInEYditWubNMw*|*server.ccl.net> X-Original-From: "tarun gupta" Content-type: multipart/alternative; boundary="Next_1138780270---0-203.199.83.39-22584" Date: 1 Feb 2006 07:51:14 -0000 MIME-Version: 1.0 Sent to CCL by: "tarun gupta" [hotbacteria|-|rediffmail.com] This is a multipart mime message --Next_1138780270---0-203.199.83.39-22584 Content-type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline =A0=0AHello everyone,=0A=0AAny one has q.kollua script in C-language. I ha= ve one in .py format but I have never worked with python. It would be bette= r if any one can send me a precompiled q.kollua in .c format.=0A=0AWhat is = the difference between q.kollua and q.amber.=0A=0A=0ARegards=0ATarun Gupta= =0A=0A=0ATarun Gupta =0D=0AB.Sc.(hons)Bioinformatics =0D=0AGGDSD College of= Post Graduation =0D=0A(Panjab University) =0D=0ASector-32/C =0D=0AChandiga= rh-160031 =0D=0AMob: +91-9888237906=0D=0A=0D=0Ahttp://www.geocities.com/hot= bacteria/aboutme.html=0D=0AHttp://360.yahoo.com/hotbacteria=0D=0Ahttp://www= .ebizwebco.com/behalbiotech/index.htm=0D=0A --Next_1138780270---0-203.199.83.39-22584 Content-type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline

=0A 
=0AHello everyone,
=0A
=0AAny one has q.kollua scrip= t in C-language. I have one in .py format but I have never worked with pyth= on. It would be better if any one can send me a precompiled q.kollua in .c = format.
=0A
=0AWhat is the difference between q.kollua and q.amber.=0A
=0A
=0ARegards
=0ATarun Gupta
=0A=0A

=0A=0A=0ATarun Gu= pta =0D
=0AB.Sc.(hons)Bioinformatics =0D
=0AGGDSD College o= f Post Graduation =0D
=0A(Panjab University) =0D
=0ASector-= 32/C =0D
=0AChandigarh-160031 =0D
=0AMob: +91-9888237906=0D
=0A=0D=
=0Ahttp://www.geocities.com/hotbacteria/aboutme.html=0D
=0AHttp://36= 0.yahoo.com/hotbacteria=0D
=0Ahttp://www.ebizwebco.com/behalbiotech/inde= x.htm=0D
=0A

=0A=0A --Next_1138780270---0-203.199.83.39-22584-- From owner-chemistry@ccl.net Wed Feb 1 10:01:00 2006 From: "Jin Hong Mei jinhm[]ihpc.a-star.edu.sg" To: CCL Subject: CCL: question to ask Message-Id: <-30738-060201030247-23153-IJU5tTo3Ph5S+qd0mwNyPw:-:server.ccl.net> X-Original-From: Jin Hong Mei Content-transfer-encoding: 7BIT Content-type: text/plain; charset=us-ascii; format=flowed Date: Wed, 01 Feb 2006 14:02:16 +0800 MIME-version: 1.0 Sent to CCL by: Jin Hong Mei [jinhm===ihpc.a-star.edu.sg] Dear Friends, I am trying to calculate the dissociation energy of H2 molecule on top of Li3N surface. I used dmol3 to do the calculations. I do find the energy barrier from adsorbed H2 molecule to dissociated 2 H atoms on Li3N surface. But I am not sure whether I got the real transitional state. I performed frequency calculations on the "transitional structures". The results showed me that there are more than one imaginary frequencies. I further analyzed all the imaginary frequencies, and found that there is only one mode related to the bond broken of H2 molecules. All others are either related to the substrate (Li3N) motion or a very slightly vibration of H2 molecules. My question is: did I find the real transitional state? Thanks a lot. Regards Hongmei ** -- ---------------------------------------------------------------------- This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you. ---------------------------------------------------------------------- From owner-chemistry@ccl.net Wed Feb 1 10:36:00 2006 From: "Ulrike Salzner salzner{=}fen.bilkent.edu.tr" To: CCL Subject: CCL:G: excited states of polyene cations Message-Id: <-30739-060201045523-32229-yZM5MJ7CuxR8oUvQcY8Kpw:server.ccl.net> X-Original-From: Ulrike Salzner Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Wed, 01 Feb 2006 10:23:13 +0200 Mime-Version: 1.0 Sent to CCL by: Ulrike Salzner [salzner^^^fen.bilkent.edu.tr] Dear collegues, I am trying to find a level theory for calculating excited states of long polyene cations. There are some issues, I would like to discuss with other people. For testing methods, I have done calculations on C12H14+ because I can also do CASSCF calculations with all pi-electrons and pi-orbitals in the active space. I am testing TDHF and TDDFT on DFT geometries of the neutral molecule. For CASSCF, I used the CASSCF structure of C12H14. UV spectra of polyenes are dominated by a strong band associated with a one-electron HOMO-LUMO transition. The open-shell cations have a similar transition at lower energy. My calculations for C12H14 give the following result: neutral: CASSCF 3.89 eV, TDHF 3.78 eV, TDDFT 3.27 eV, exp: 3.41 eV in solution, ~ 3.7 eV gas phase cation: CASSCF(11,12) 1.45 eV orbitals 1-4 occupied by about 2 electrons, 5: 1.33 e, 6: 1.21 e, 7: 0.47 e, 8: 0.11 e, 9-12 under 0.1 e TDHF: 1) 1.40 eV oscillator strength 1.95, main transitions: HOMO-alpha- LUMO-alpha (0.93), HOMO-beta-LUMO-beta (0.86) 2) 3.06 eV oscillator strength 0.04, main transitions: HOMO-alpha-LUMO- alpha (-0.66), HOMO-beta-LUMO-beta (0.75) With DFT, the two states are inversed: TDDFT: 1) 1.56 eV oscillator strength 0.01, main transitions: HOMO- alpha-LUMO-alpha (-0.79), HOMO-beta-LUMO-beta (0.77) 2) 2.42 eV oscillator strength 2.16, main transitions: HOMO-alpha-LUMO- alpha (0.60), HOMO-beta-LUMO-beta (0.60) Thus both, TDHF and TDDFT give two transitions combined of HOMO-LUMO transitions in alpha and beta spaces. One has the same sign for alpha and beta and one has opposite signs, the latter having low oscillator strength. However, TDHF gives the lower energy to the transition with same sign and TDDFT does the opposite. One would predict therefore very different spectra at both levels of theory. From comparison with a series of other calculations, the TDDFT results appears to be very reasonable. To find out why there is such a difference, I checked the orbitals. The order is the same for all occupied and the lower three pi-orbitals at both levels of theory (AU, BG, AU, BG,...). With TDHF, the HOMO-LUMO gap between alpha orbitals is smaller than between beta orbitals, with TDDFT it is reversed. Does anyone have an idea what is going on? I think these methods are not intended for open-shell calculations (I am using G03), this is why I am testing the outcome. Higher excited state with CASSCF are running right now. I can see from the CASSCF calculation that the first excited state is also a HOMO-LUMO transition of alpha and beta electrons, but how can I find out the signs to compare them with TD results? My last question is concerned with the CI coefficients: With TDHF, the squares of the coefficients sum up to more than 1 even if I add the alpha and beta coefficients belonging to the same excited state separately. I thought that the sum of the coefficients is normalized to 1. Is this wrong? This was a bit long, but if anyone is interested in this topic, we could also start some colaboration. Any adivice is highly appreciated. Thanks, Ulrike -- Ulrike Salzner Associate Professor Department of Chemistry Bilkent University 06800 Bilkent, Ankara Turkey From owner-chemistry@ccl.net Wed Feb 1 11:11:01 2006 From: "Gonalo Justino goncalo.justino---zmail.pt" To: CCL Subject: CCL: radicals in MOPAC Message-Id: <-30740-060201084956-6381-c1EMeVWgEgs1Z+ilULkaUA~~server.ccl.net> X-Original-From: "Gonalo Justino" Sent to CCL by: "Gonalo Justino" [goncalo.justino~!~zmail.pt] Hi all, I'm having a strange issue with MOPAC working on radicals. I have a C15O7H9(.-) radical (and others like this) and I can't get any calculations done with any version of MOPAC on AM1, but other radicals like methyl and superoxide and the parent C15O7H10 work just fine. The issue is that any keword combination I've tried (using OPEN, C.I. and/or others) produces either error messages or weird software behaviour. My questions are: 1. what keywords could you recommend me? 2. if not a keyword, what could be the problem? Any help would be very welcome, Best wishes, Gonalo ________________________ Gonalo Justino goncalo.justino]|[zmail.pt From owner-chemistry@ccl.net Wed Feb 1 11:45:00 2006 From: "andras.borosy::givaudan.com" To: CCL Subject: CCL: Quick Time movies by Moviemaker at Octane (IRIX 6.5.18) Message-Id: <-30741-060201093420-25009-3G6L2CnMl2KjM0DLj2Qb8A||server.ccl.net> X-Original-From: andras.borosy**givaudan.com Content-Type: multipart/alternative; boundary="=_alternative 00500B71C1257108_=" Date: Wed, 1 Feb 2006 15:34:00 +0100 MIME-Version: 1.0 Sent to CCL by: andras.borosy|*|givaudan.com This is a multipart message in MIME format. --=_alternative 00500B71C1257108_= Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable Dear Colleagues, I have created Quick Time movies by Moviemaker at my Octane (IRIX 6.5.18)=20 which can not be played outside Silicon Graphics (in .mov and .avi), or=20 their quality is very bad (in .mpeg). What can I do? Regards, Dr. Andr=E1s P=E9ter Borosy Senior Scientist Fragrance Research Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - D=FCbendorf -= =20 Switzerland T:+41-1-824 2164 - F:+41-1-8242926 - http://www.givaudan.com --=_alternative 00500B71C1257108_= Content-Type: text/html; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable

Dear Colleagues,

I have created Quick Time movies by Moviemaker at my Octane (IRIX 6.5.18) which can not be played  outside Silicon Graph= ics (in .mov and .avi), or their quality is very bad (in .mpeg). What can I do?

Regards,

Dr. Andr=E1s P=E9ter Borosy
Senior Scientist
Fragrance Research
Givaudan Schweiz AG  -  Ueberlandstrasse 138  -  CH-8600  -  D=FCbendorf  -  Switzerland
T:+41-1-824 2164  -  F:+41-1-8242926    -  http://= www.givaudan.com --=_alternative 00500B71C1257108_=-- From owner-chemistry@ccl.net Wed Feb 1 12:20:01 2006 From: "Pascal Gosselin gosselin{=}univ-lemans.fr" To: CCL Subject: CCL: Radical Stabilization Energy vs SOMO-LUMO Gap Message-Id: <-30742-060201103719-8930-gvYzmRPICXn7A6GVaHdnhA(-)server.ccl.net> X-Original-From: "Pascal Gosselin" Sent to CCL by: "Pascal Gosselin" [gosselin_._univ-lemans.fr] Dear All, I am currently evaluating (HF/3-21G) the resonance stabilization energy of unsaturated radicals via the following isodesmic reaction: RCH3 + CH3rad -> RCH2rad + CH4 (according to Ochiai, Tomita and Endo, Macromol. 34(6) 1634 (2001). This constitutes a Case Study on page 199 of Cramer's Computational Chemistry book (2nd Ed.) Thanks to MacSpartan'04 spreadsheet facility, I put side by side the calculated stabilization energy for various RCH2rad and the SOMO-LUMO Gap for the same radical (6 examples). Both series look like varying in the same manner. To confirm this impression, I asked for the corresponding plot and obtained a Linear LSQ fit with R2 = 0.990 ! Such a good linear correlation is astonishing, no? Could anyone help me to interpret this correlation between the RSE and the Gap? Many thanks, Regards, From owner-chemistry@ccl.net Wed Feb 1 12:55:00 2006 From: "Harald Lanig Harald.Lanig-$-chemie.uni-erlangen.de" To: CCL Subject: CCL: Beilstein Bozen Workshop 2006 Message-Id: <-30743-060201113726-18590-o2DZuQcbvSpEAgwV5k6flQ],[server.ccl.net> X-Original-From: Harald Lanig Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1; format=flowed Date: Wed, 01 Feb 2006 17:37:10 +0100 MIME-Version: 1.0 Sent to CCL by: Harald Lanig [Harald.Lanig::chemie.uni-erlangen.de] - Apologies for any cross-postings - We would like to inform you that registration has started for our forthcoming workshop: Molecular Interactions - Bringing Chemistry to Life May 15th - 19th, 2006, Bozen, Italy www.beilstein-institut.de The Beilstein workshops address contemporary issues in the chemical and related sciences by employing an interdisciplinary approach. Scientists > from a wide range of areas ­ often outside chemistry ­ are invited to present aspects of their work for discussion with the aim of not only to advance science, but also, to enhance interdisciplinary communication. The workshop will take place in the historic Hotel Schloss Korb. The setting and the limited number of participants (ca. 50-60), provide a very convivial atmosphere for the ready exchange of thoughts and ideas. Please find further general information, the scientific program, the first circular and the registration form on our web site: www.beilstein-institut.de/events Places at the workshop are limited and will be allocated on a first-come basis. Please feel free to pass on the information to colleagues whom you think would also be interested in attending. We would be delighted to see you in Bozen. We have an excellent line-up of speakers including: Tom Blundell (Cambridge) Protein-protein interactions in cell regulation and signalling: targets for drug discovery Wilhelm Boland (MPI Jena) Herbivore-induced volatiles in plant defence: early and late events in enemy-recognition and response Tim Clark (Erlangen) Biological communication via molecular surfaces Jonathan Clayden (Manchester) Remote control of stereochemistry: communicating information via conformation Athel Cornish-Bowden (CNRS Marseille) Bringing chemistry to life: what does it mean to be alive? Jonathan Essex (Southampton) Coarse-grained modelling of membrane systems Richard Goldstein (NMIR London) Modelling the evolution of influenza Stephen Haggarty (Broad Institute, Cambridge) The principle of complementarity: chemical versus biological space Andreas Hirsch (Erlangen) Artificial micelles and liposomes Trevor Howe (Janssen, Beerse) Interpretation of drug discovery data through visualization; current issues Sijbren Otto (Cambridge) Bringing supramolecular chemistry to life Joelle N. Pelletier (Montreal) Modifying enzyme specificity by combinatorial active site mutations Laurent M. Humeau (VIRxSYS, Gaithersburg) From the bench to the clinic: story and lessons from VRX496, the first lentivector ever tested in phase 1 clinical trial Mark Sansom (Oxford) Molecular simulations of membrane proteins Gisbert Schneider (Frankfurt) Designing natural product-derived focused libraries ----------------------------------------- Martin G. Hicks Beilstein-Institut Trakehnerstr. 7-9 60487 Frankfurt Germany tel: +49 69 7167 3220 fax: +49 69 7167 3219 ----------------------------------------- From owner-chemistry@ccl.net Wed Feb 1 13:30:01 2006 From: "Dr Nageswar drnageswar##yahoo.com" To: CCL Subject: CCL: [Fwd: Parameters for Selinium] Message-Id: <-30744-060201113436-17857-MEAxJg+sxvq2MVgktdvekA^server.ccl.net> X-Original-From: Dr Nageswar Content-Transfer-Encoding: 8bit Content-Type: multipart/mixed; boundary="0-460674233-1138808069=:95692" Date: Wed, 1 Feb 2006 07:34:29 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Dr Nageswar [drnageswar{}yahoo.com] --0-460674233-1138808069=:95692 Content-Type: multipart/alternative; boundary="0-2058069885-1138808069=:95692" --0-2058069885-1138808069=:95692 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Note: forwarded message attached. --------------------------------- Bring words and photos together (easily) with PhotoMail - it's free and works with Yahoo! Mail. --0-2058069885-1138808069=:95692 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit


Note: forwarded message attached.

Bring words and photos together (easily) with
PhotoMail - it's free and works with Yahoo! Mail. --0-2058069885-1138808069=:95692-- --0-460674233-1138808069=:95692 Content-Type: message/rfc822 X-Apparently-To: drnageswar],[yahoo.com via 209.191.85.114; Wed, 01 Feb 2006 05:45:22 -0800 X-Originating-IP: [66.93.212.15] Authentication-Results: mta208.mail.mud.yahoo.com from=ccl.net; domainkeys=neutral (no sig) Received: from 66.93.212.15 (EHLO server.ccl.net) (66.93.212.15) by mta208.mail.mud.yahoo.com with SMTP; Wed, 01 Feb 2006 05:43:41 -0800 Received: from server.ccl.net (ccl [127.0.0.1]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id k11DhZDU005971 for ; Wed, 1 Feb 2006 08:43:36 -0500 Received: from 66.93.212.3 (SquirrelMail authenticated user ccl) by server.ccl.net with HTTP; Wed, 1 Feb 2006 08:43:36 -0500 (EST) Date: Wed, 1 Feb 2006 08:43:36 -0500 (EST) Subject: [Fwd: Parameters for Selinium] > From: "Computational Chemistry List" To: "Dr Nageswar" Reply-To: ccl],[ccl.net User-Agent: SquirrelMail/1.4.6 [CVS]-0.cvs20050812.1.fc3 MIME-Version: 1.0 Content-Type: multipart/mixed;boundary="----=_20060201084336_63512" X-Priority: 3 (Normal) Importance: Normal X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED,HTML_30_40, HTML_MESSAGE autolearn=failed version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Content-Length: 833 ------=_20060201084336_63512 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit To send mail to CCL subscribers, please address it to: chemistry],[ccl.net or use the mail sending Web form available from the CCL Home page: http://www.ccl.net Jan ---------------------------- Original Message ---------------------------- Subject: Parameters for Selinium > From: "Dr Nageswar" Date: Wed, February 1, 2006 5:44 am To: ccl],[ccl.net -------------------------------------------------------------------------- Hello, I am working on AMBER force field. I had Selinium (Se) atom attached to C (SP3) in one case and in another case it is attached to C (SP) for my proposed ligands. If you can give all the parameters for Se, I am greatful for your help. Regards Nageswar --------------------------------- Bring words and photos together (easily) with PhotoMail - it's free and works with your Yahoo! Mail. -- Computational Chemistry List Attn. Jan K. Labanowski Columbus, OH 43221 http://www.ccl.net E-mail: chemistry-request],[ccl.net or ccl],[ccl.net ------=_20060201084336_63512 Content-Type: text/html; name="untitled-2" Content-Transfer-Encoding: 8bit Content-Disposition: attachment; filename="untitled-2"
Hello,
 
I am working on AMBER force field. I had Selinium (Se) atom attached to C (SP3) in one case and in another case it is attached to C (SP) for my proposed ligands. If you can give all the parameters for Se, I am greatful for your help.
 
Regards
Nageswar

Bring words and photos together (easily) with
PhotoMail - it's free and works with your Yahoo! Mail. ------=_20060201084336_63512-- --0-460674233-1138808069=:95692-- From owner-chemistry@ccl.net Wed Feb 1 14:09:09 2006 From: "James J. P. Stewart mrmopac]=[worldnet.att.net" To: CCL Subject: CCL: radicals in MOPAC Message-Id: <-30745-060201131543-24636-oFKsG/REuSfGfWurLNId+w^_^server.ccl.net> X-Original-From: "James J. P. Stewart" Content-Type: multipart/alternative; boundary="=====================_618077668==.ALT" Date: Wed, 01 Feb 2006 11:15:20 -0700 Mime-Version: 1.0 Sent to CCL by: "James J. P. Stewart" [mrmopac : worldnet.att.net] --=====================_618077668==.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed At 09:12 AM 2/1/2006, you wrote: >Sent to CCL by: "Gonalo Justino" [goncalo.justino~!~zmail.pt] >Hi all, > >I'm having a strange issue with MOPAC working on radicals. I have a >C15O7H9(.-) radical (and others like this) and I can't get any >calculations done with any version of MOPAC on AM1, but other >radicals like methyl and superoxide and the parent C15O7H10 work >just fine. The issue is that any keword combination I've tried >(using OPEN, C.I. and/or others) produces either error messages or >weird software behaviour. My questions are: If you're not specifically interested in electronic states, use keyword UHF. If you still have problems, contact me direct. Jimmy ( |-| |-| ) .-----------------oOOo----(_)----oOOo--------------------------------------. | James J. P. Stewart | | | Stewart Computational Chemistry LLC | E-mail: mrmopac|-|worldnet.att.net | | 15210 Paddington Circle | 39/03/15 N, 104/49/29 W | | Colorado Springs CO 80921-2512 | | | USA .ooo0 | Phone: USA +(719) 488-9416 | | ( ) Oooo. | | .------------------------\ (----( )--------------------------------------. \_) ) / (_/ --=====================_618077668==.ALT Content-Type: text/html; charset="us-ascii" At 09:12 AM 2/1/2006, you wrote:
Sent to CCL by: "Gonalo  Justino" [goncalo.justino~!~zmail.pt]
Hi all,

I'm having a strange issue with MOPAC working on radicals. I have a C15O7H9(.-) radical (and others like this) and I can't get any calculations done with any version of MOPAC on AM1, but other radicals like methyl and superoxide and the parent C15O7H10 work just fine. The issue is that any keword combination I've tried (using OPEN, C.I. and/or others) produces either error messages or weird software behaviour. My questions are:

If you're not specifically interested in electronic states, use keyword UHF.

If you still have problems, contact me direct.

Jimmy


                         ( |-| |-| )
 .-----------------oOOo----(_)----oOOo--------------------------------------.
 | James J. P. Stewart                 |                                    |
 | Stewart Computational Chemistry LLC | E-mail:  mrmopac|-|worldnet.att.net  |
 | 15210 Paddington Circle             |  39/03/15 N, 104/49/29 W           |
 | Colorado Springs CO 80921-2512      |                                    |
 | USA                   .ooo0         | Phone: USA +(719) 488-9416         |
 |                       (   )   Oooo. |                                    |
 .------------------------\ (----(   )--------------------------------------.
                           \_)    ) /
                                 (_/ --=====================_618077668==.ALT-- From owner-chemistry@ccl.net Wed Feb 1 15:29:01 2006 From: "Van Dam, HJJ \(Huub\) h.j.j.vandam#%#dl.ac.uk" To: CCL Subject: CCL:G: excited states of polyene cations Message-Id: <-30746-060201120411-9102-hdmZkoUux/sNt3uqlXp7mw---server.ccl.net> X-Original-From: "Van Dam, HJJ \(Huub\)" Content-Class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 1 Feb 2006 16:28:17 -0000 MIME-Version: 1.0 Sent to CCL by: "Van Dam, HJJ \(Huub\)" [h.j.j.vandam-,-dl.ac.uk] Hi Ulrike, With respect to your particular application I cannot say much. On the question of the norm of the resulting vectors I can say that assuming that you are solving RPA type equations the basic equation is of the form: (A B)(X) (1 0)(X) ( )( )= E( )( ) (B A)(Y) (0 -1)(Y) Where E is your excitation energy. The fact that you have a -1 in the matrix on the right-hand-side of the equation leads to the eigenvectors to be normalised as X*X - Y*Y = 1 The vectors X and Y in your case will contain both alpha and beta components. I am not sure how identify the vectors X and Y in a Gaussian output though. I hope this helps, Huub ========================================================== Huub van Dam (h.j.j.vandam(a)dl.ac.uk, +44-1925-603933) ========================================================== -----Original Message----- > From: owner-chemistry(a)ccl.net [mailto:owner-chemistry(a)ccl.net] Sent: 01 February 2006 15:37 To: Vandam, Huub Subject: CCL:G: excited states of polyene cations Sent to CCL by: Ulrike Salzner [salzner^^^fen.bilkent.edu.tr] Dear collegues, ... My last question is concerned with the CI coefficients: With TDHF, the squares of the coefficients sum up to more than 1 even if I add the alpha and beta coefficients belonging to the same excited state separately. I thought that the sum of the coefficients is normalized to 1. Is this wrong? This was a bit long, but if anyone is interested in this topic, we could also start some colaboration. Any adivice is highly appreciated. Thanks, Ulrike -- Ulrike Salzner Associate Professor Department of Chemistry Bilkent University 06800 Bilkent, Ankara Turkeyhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Wed Feb 1 16:04:00 2006 From: "Xiaowei (David) Li xl3a : virginia.edu" To: CCL Subject: CCL: Software for calculating Circular Dichroism of DNA Message-Id: <-30747-060201123549-31435-6wKlPeCehOBljORFADvong() server.ccl.net> X-Original-From: "Xiaowei (David) Li" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 01 Feb 2006 11:32:07 -0500 MIME-Version: 1.0 Sent to CCL by: "Xiaowei (David) Li" [xl3a/./virginia.edu] Dear CCL members: Could anyone recommend me a software or package for calculating the Circular Dichroism spectrum of DNA? I am currently measuring the CD of DNA oligomers. But I am very interested in comparing the experimental results with the theoretical results. Thank you in advance. Best, Xiaowei Li Department of Electrical and Computer Engineering University of Virginia From owner-chemistry@ccl.net Wed Feb 1 17:36:00 2006 From: "Jozsef Csontos jozsefcsontos~~creighton.edu" To: CCL Subject: CCL: PES vs. # of CPUs Message-Id: <-30748-060201171851-9495-pZU31dnbQER9LD3vfBYgSQ|-|server.ccl.net> X-Original-From: Jozsef Csontos Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Wed, 01 Feb 2006 14:57:14 -0600 Mime-Version: 1.0 Sent to CCL by: Jozsef Csontos [jozsefcsontos]|[creighton.edu] Hi, my short question is: is it possible to get different optimized final structures using the same input and architecture, OS, software (and so on), but different number of processors? My longer comments are: I understand that we use approximations (in QM and in life too:) and there might be error accumulations and our number representation depends on the hardware etc. But, I'm quite sure the answer is no. Maybe I'm wrong, so I tell you the story. The story: I have been using a commercial quantum package, which uses the MPI libraries (MPICH) for parallelization. I was about to map the PES of several tripeptides in water using DFT. (Of course, the molecules are flexible and the PESs are flat and more more approximations) I'm not totally surprised that the results are different on 1 node with 1 processor and 6 node with 6 processors. (In the first case there is no MPI and in the second one there is.) Interestingly, the results are different on 3 nodes with 6 processors (2CPUs/node) and on 6 nodes with 6 processors (1CPU/node), in addition the calculation using the previous 6 processor configuration (2CPUs/node) differs from the 4 CPUs config (2CPUs/node) ones. The energy differences between the structures are small about 1kcal/mol, however, the rmsd is quite large 1.9 Angstrom considering heavy atoms and one of these structures is the deepest minimum on the PES, so these structures belong to the low energy region. I haven't checked all the structures whether they are minima or other stationary points. I guess this is not related to the question, but if all of them were minima my question would be louder. I'm wondering what your opinions are? Best wishes, Jozsef -- Jozsef Csontos, Ph.D. Department of Biomedical Sciences Creighton University, Omaha, NE From owner-chemistry@ccl.net Wed Feb 1 20:51:00 2006 From: "Eric Scerri scerri/a\chem.ucla.edu" To: CCL Subject: CCL: invitation to submit an article or commentary on a topic of chemical interest Message-Id: <-30749-060201194921-7628-tvgWYgaXviiiv2ZuBR7q7g:_:server.ccl.net> X-Original-From: Eric Scerri Content-Type: multipart/alternative; boundary=Apple-Mail-1--530863868 Date: Wed, 1 Feb 2006 15:46:49 -0800 Mime-Version: 1.0 (Apple Message framework v746.2) Sent to CCL by: Eric Scerri [scerri(a)chem.ucla.edu] --Apple-Mail-1--530863868 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed You are invited to submit an article or commentary for publication to the Springer journal, Foundations of Chemistry website: http://www.springer.com/sgw/cda/frontpage/0,11855,4-40399-70-35545882- detailsPage%253Djournal%257CmostViewedArticles%257CmostViewedArticles, 00.html then go to "instructions for authors" or "online version" to view tables of contents and past issues. The scope of the journal includes history of chemistry, philosophy of chemistry, chemical education, computational/theoretical chemistry etc. Dr. Eric Scerri, Department of Chemistry & Biochemistry, UCLA, Los Angeles, CA 90095-1569 E-mail scerri|*|chem.ucla.edu Tel: 310 206 7443 UCLA faculty web page: http://www.chem.ucla.edu/dept/Faculty/scerri/ Editor of Foundations of Chemistry, http://www.springer.com/sgw/cda/frontpage/0,11855,4-40399-70-35545882- detailsPage%253Djournal%257CmostViewedArticles%257CmostViewedArticles, 00.html International Society for the Philosophy of Chemistry, http://ispc.sas.upenn.edu/ --Apple-Mail-1--530863868 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1



You are invited to submit an = article or commentary for publication to the Springer journal,


=A0Foundations of = Chemistry

website:

then go to "instructions for authors"=A0 = or=A0=A0"online = version" to view tables of contents and past = issues.


The scope of the journal = includes history of chemistry, philosophy of chemistry, chemical = education, computational/theoretical chemistry etc.=A0





Dr. Eric = Scerri,
Department of Chemistry & = Biochemistry,
UCLA,
Los Angeles,
CA = 90095-1569

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= --Apple-Mail-1--530863868-- From owner-chemistry@ccl.net Wed Feb 1 21:25:00 2006 From: "Marcin Makowski makowskm\a/chemia.uj.edu.pl" To: CCL Subject: CCL: excited states of polyene cations Message-Id: <-30750-060201205049-12715-lSavQdbgNqz9rAZl5pJVWQ**server.ccl.net> X-Original-From: "Marcin Makowski" Sent to CCL by: "Marcin Makowski" [makowskm|a|chemia.uj.edu.pl] Dear Ulrike, TDDFT usually gives wrong description of relative enegies of A_g and B_u states of neutral polyenes. There was a paper by Head-Gordon showing that Tamm-Dancoff approximation to TDDFT works better in this case than popular RPA, but still this does not seem to be a method of choice for these systems, probably. CASSCF worked quite fine as long as large active space can be used. I remember one paper pointing that you need sth like double-zeta active space (for octatetraene it would be 4 occupied, 8 virtual) to obtain very good accuracy. I can search for reference if you are interested. It was so as I've checked up to C10. I was testing some time ago CIS(D) and SAC-CI but they still had big problems with A_g state (the one dominated by double excitation). The similar problems might happen for cations - this is out of my knowledge (I did not make any calculations on them). Yours, Marcin Makowski -- Dr Marcin Makowski Jagiellonian University Department of Theoretical Chemistry email:makowskm**chemia.uj.edu.pl or Kyushu University email:marcin**cube.kyushu-u.ac.jp From owner-chemistry@ccl.net Wed Feb 1 22:00:01 2006 From: "janl%x%speakeasy.net" To: CCL Subject: CCL: PES vs. # of CPUs Message-Id: <-30751-060201210340-20628-ThTYOxmeFBBtcSpGE8wULw%%server.ccl.net> X-Original-From: janl^-^speakeasy.net Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 02 Feb 2006 02:03:33 +0000 MIME-Version: 1.0 Sent to CCL by: janl ~ speakeasy.net While very small differences (truncation errors) are allowed between single processor and parallel runs (they may be due to some rounding errors when data are being sent between processors or machines), they should be below 0.001 kcal/mol. The differences 1000x larger indicate one or more: 1) Bug in the program 2) Bug in the compilation or compiler 3) Bug in the MPICH libraries 4) Faults in configuration 5) Errors in communications, e.g., lost packets, or connectionless protocol (use TCP for testing, rather then UDP if you have a choice of configuration). Jan Labanowski jkl!=!ccl.net > -----Original Message----- > From: Jozsef Csontos jozsefcsontos~~creighton.edu [mailto:owner-chemistry!=!ccl.net] > Sent: Wednesday, February 1, 2006 10:52 PM > To: 'Labanowski, Jan - > Subject: CCL: PES vs. # of CPUs > > Sent to CCL by: Jozsef Csontos [jozsefcsontos]|[creighton.edu] > Hi, > > my short question is: > is it possible to get different optimized final structures using the > same input and architecture, OS, software (and so on), but different > number of processors? > > My longer comments are: > I understand that we use approximations (in QM and in life too:) and > there might be error accumulations and our number representation depends > on the hardware etc. But, I'm quite sure the answer is no. Maybe I'm > wrong, so I tell you the story. > > The story: > I have been using a commercial quantum package, which uses the MPI > libraries (MPICH) for parallelization. I was about to map the PES of > several tripeptides in water using DFT. (Of course, the molecules are > flexible and the PESs are flat and more more approximations) I'm not > totally surprised that the results are different on 1 node with 1 > processor and 6 node with 6 processors. (In the first case there is no > MPI and in the second one there is.) Interestingly, the results are > different on 3 nodes with 6 processors (2CPUs/node) and on 6 nodes with > 6 processors (1CPU/node), in addition the calculation using the previous > 6 processor configuration (2CPUs/node) differs from the 4 CPUs config > (2CPUs/node) ones. > The energy differences between the structures are small about 1kcal/mol, > however, the rmsd is quite large 1.9 Angstrom considering heavy atoms > and one of these structures is the deepest minimum on the PES, so these > structures belong to the low energy region. I haven't checked all the > structures whether they are minima or other stationary points. I guess > this is not related to the question, but if all of them were minima my > question would be louder. > > I'm wondering what your opinions are? > > Best wishes, > > Jozsef > > -- > Jozsef Csontos, Ph.D. > > Department of Biomedical Sciences > Creighton University, > Omaha, NE >