From owner-chemistry@ccl.net Fri Mar 16 01:07:01 2007 From: "Mike hang mikehang2007=-=yahoo.com" To: CCL Subject: CCL:G: what is the best choice of memory size in Gaussian 03 Message-Id: <-33811-070316010238-3422-BQi/b3kuMDxR9NvKKt1zxA++server.ccl.net> X-Original-From: Mike hang Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1812276511-1174021338=:37505" Date: Thu, 15 Mar 2007 22:02:18 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Mike hang [mikehang2007.++.yahoo.com] --0-1812276511-1174021338=:37505 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit The question that one should pose is not what is the best choice of memory size but what is the right choice of memory size. The right choice entirely depend on the molecule and type of calculation or basis set considered. Larger basis set will take greater memory. As an example consider a simple molecule H2: suppose that you perform Opt calculation with %mem=500mb It will take 8 minute but with only %mem=25mb, it will take 1 minute. well the question that you must be posing to yourself is that how to determine the right memory choice. this will come by experience OR use the "NReq" approach which can be found from the link below http://www.hpc.uio.no/notur/gaussbench/mem.php hope that this will help mike On Wed, 2007-03-14 at 03:09, Jeon Hwan Jeon jullujet-$-graceldisplay.com wrote: > Sent to CCL by: "Jeon Hwan Jeon" [jullujet]~[graceldisplay.com] > Please help me~~~~~~ > > I use Gaussian 03 for LINUX and now my OS is Fedora Core 3. > > Thoghth I used to calc many molecules, thses days,I knew that all my input files are not good! > > Because my way to use memory is fault! > > For example, when I calculate big size molecule such as antrcene, I make like this. > > ----------- > > %mem=950MB > b3lyp/6-311++g** opt freq=noraman > > title > > 0 1 > > ------------ > > > My system's physical memory is 1GB, so I use 950MB. > > But It's slow than 6MW, 48MB...!! > > I can't understand this situation. > > Why small size memory calc. speed is slower than large size memory? > > How can I make good input file? > > I saw the tips in Gaussian Manual. But I can't understant those. > > What is M + 2Nb2? > > When I use " 6-311++G(d,p) (5D, 7F) 187 basis functions ", what is the best choice about %mem... > > > please help me.... > > > p.s my English is too bad... T.Thttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--------------------------------- Get your own web address. Have a HUGE year through Yahoo! Small Business. --0-1812276511-1174021338=:37505 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit The question that one should pose is not what is the best choice of memory size but what is the right choice of memory size. The right choice entirely depend on the molecule and type of calculation or basis set considered. Larger basis set will take greater memory. As an example consider a simple molecule H2: suppose that you perform Opt calculation with %mem=500mb It will take 8 minute but with only %mem=25mb, it will take 1 minute. well the question that you must be posing to yourself is that how to determine the right memory choice. this will come by experience OR use the
"NReq" approach which can be found from the link below

http://www.hpc.uio.no/notur/gaussbench/mem.php

hope that this will help
mike


On Wed, 2007-03-14 at 03:09, Jeon Hwan Jeon jullujet-$-graceldisplay.com
wrote:
> Sent to CCL by: "Jeon Hwan Jeon" [jullujet]~[graceldisplay.com]
> Please help me~~~~~~
>
> I use Gaussian 03 for LINUX and now my OS is Fedora Core 3.
>
> Thoghth I used to calc many molecules, thses days,I knew that all my input files are not good!
>
> Because my way to use memory is fault!
>
> For example, when I calculate big size molecule such as antrcene, I make like this.
>
> -----------
>
> %mem=950MB
> b3lyp/6-311++g** opt freq=noraman
>
> title
>
> 0 1
>
> ------------
>
>
> My system's physical memory is 1GB, so I use 950MB.
>
> But It's slow than 6MW, 48MB...!!
>
> I can't understand this situation.
>
> Why small size memory calc. speed is slower than large size memory?
>
> How can I make good input file?
>
> I saw the tips in Gaussian Manual. But I can't understant those.
>
> What is M + 2Nb2?
>
> When I use " 6-311++G(d,p) (5D, 7F) 187 basis functions ", what is the best choice about %mem...
>
>
> please help me....
>
>
> p.s my English is too bad... T.T





Get your own web address.
Have a HUGE year through Yahoo! Small Business. --0-1812276511-1174021338=:37505-- From owner-chemistry@ccl.net Fri Mar 16 01:42:00 2007 From: "Fan,Huajun hjfan^^^pvamu.edu" To: CCL Subject: CCL: program to split sdf file Message-Id: <-33812-070316013849-17333-yFp4oqOFGPa1RbDFWoey0A:+:server.ccl.net> X-Original-From: "Fan,Huajun" Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C7678D.56FBF4A0" Date: Fri, 16 Mar 2007 00:38:35 -0500 MIME-Version: 1.0 Sent to CCL by: "Fan,Huajun" [hjfan .. pvamu.edu] This is a multi-part message in MIME format. ------_=_NextPart_001_01C7678D.56FBF4A0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Hi, Does anyone know any programs (preferably free) that can split a big sdf file into smaller files? I got a sdf file containing 30,000 molecules and want to do a DOCK5. It is too big even to read it through. I want to split it into 10 samller files that contains 3,000 each. Is it possible? The newest version of Babel seems not available of this split function for SDF format. =20 Thanks in advance. =20 Hua-Jun=20 =20 ------_=_NextPart_001_01C7678D.56FBF4A0 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Hi, Does anyone know any programs (preferably free) = that can split a big sdf file into smaller files? I got a sdf file containing = 30,000 molecules and want to do a DOCK5. It is too big even to read it through. = I want to split it into 10 samller files that contains 3,000 each. Is it = possible? The newest version of = Babel seems not available of this = split function for SDF format.

 

Thanks in advance.

 

Hua-Jun =

 

------_=_NextPart_001_01C7678D.56FBF4A0-- From owner-chemistry@ccl.net Fri Mar 16 07:38:01 2007 From: "Demetrios Xenides qc2]^[chemistry.upatras.gr" To: CCL Subject: CCL: program to split sdf file Message-Id: <-33813-070316073522-11959-/gIB04YMCBgb1IIBmESwiA_+_server.ccl.net> X-Original-From: Demetrios Xenides Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 16 Mar 2007 12:33:53 +0200 MIME-Version: 1.0 Sent to CCL by: Demetrios Xenides [qc2(0)chemistry.upatras.gr] Fan,Huajun hjfan^^^pvamu.edu wrote: > > Hi, Does anyone know any programs (preferably free) that can split a > big sdf file into smaller files? I got a sdf file containing 30,000 > molecules and want to do a DOCK5. It is too big even to read it > through. I want to split it into 10 samller files that contains 3,000 > each. Is it possible? The newest version of Babel seems not available > of this split function for SDF format. > > > > Thanks in advance. > > > > **Hua-Jun ** > > > !!!!!Before do anything backup your file!!!! some not so "automatic" solution (it applies only in linux, unix) might be the following: (suppose that you have a console open, then) 1) wc -l name_of_file (then you get the number of lines) 2) starting from the top: head -n 1000 name_of_file>name_of_fileXXXX (repeat by changing the name name_of_fileXXXX for every "head") or 2) starting from the bottom: tail -f -n 1000 name_of_file>name_of_fileXXXX (repeat by changing the name name_of_fileXXXX for every "tail") Cheers D From owner-chemistry@ccl.net Fri Mar 16 08:43:00 2007 From: "=?iso-8859-1?Q?Mads_N=F8rregaard-Madsen?= MN.|,|.nuevolution.com" To: CCL Subject: CCL: program to split sdf file Message-Id: <-33814-070316042505-30911-KHIFoPfBwp2c13Y7XL4TnA|,|server.ccl.net> X-Original-From: =?iso-8859-1?Q?Mads_N=F8rregaard-Madsen?= Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C767A0.04B210D6" Date: Fri, 16 Mar 2007 08:52:16 +0100 MIME-Version: 1.0 Sent to CCL by: =?iso-8859-1?Q?Mads_N=F8rregaard-Madsen?= [MN#,#nuevolution.com] This is a multi-part message in MIME format. ------_=_NextPart_001_01C767A0.04B210D6 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi, =20 You could try ChemFileBrowser - www.hyleos.net =20 =20 /Mads =20 ________________________________ > From: owner-chemistry-$-ccl.net [mailto:owner-chemistry-$-ccl.net]=20 Sent: Friday, March 16, 2007 6:39 AM To: Mads N=F8rregaard-Madsen Subject: CCL: program to split sdf file =20 Hi, Does anyone know any programs (preferably free) that can split a big = sdf file into smaller files? I got a sdf file containing 30,000 = molecules and want to do a DOCK5. It is too big even to read it through. = I want to split it into 10 samller files that contains 3,000 each. Is it = possible? The newest version of Babel seems not available of this split = function for SDF format. =20 Thanks in advance. =20 Hua-Jun=20 =20 ------_=_NextPart_001_01C767A0.04B210D6 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Hi,

 

You could try ChemFileBrowser – www.hyleos.net

 =

/Mads

 

From: owner-chemistry-$-ccl.net [mailto:owner-chemistry-$-ccl.net]
Sent: Friday, March 16, = 2007 6:39 AM
To: Mads N=F8rregaard-Madsen
Subject: CCL: program to = split sdf file

 

Hi, Does anyone know any programs (preferably = free) that can split a big sdf file into smaller files? I got a sdf file = containing 30,000 molecules and want to do a DOCK5. It is too big even to read it = through. I want to split it into 10 samller files that contains 3,000 each. Is it possible? The newest = version of Babel seems not = available of this split function for SDF = format.

 

Thanks in = advance.

 

Hua-Jun =

 

------_=_NextPart_001_01C767A0.04B210D6-- From owner-chemistry@ccl.net Fri Mar 16 09:17:00 2007 From: "Piotr K. Wawrzyniak p.k.wawrzyniak++chem.leidenuniv.nl" To: CCL Subject: CCL: electronic density difference - how not to reorient molecules (G03) Message-Id: <-33815-070316091325-21480-8d9f5pnRL43vwvi+/UQNUQ#server.ccl.net> X-Original-From: "Piotr K. Wawrzyniak" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Fri, 16 Mar 2007 13:42:36 +0100 MIME-Version: 1.0 Sent to CCL by: "Piotr K. Wawrzyniak" [p.k.wawrzyniak\a/chem.leidenuniv.nl] Hello Tapas, I'd never thought that reorientation comes because of the symmetry :) Thanks for your help, now the things will work correctly. Regards, Piotr Quoting "Tapas Kar tapaskar*cc.usu.edu" : > Sent to CCL by: "Tapas Kar" [tapaskar**cc.usu.edu] > Hi Piotr > "nosym" in route card will not reorient the molecules. > > BLYP/6-311++G(d,p) SP Density=current Population=(ESP,Regular) nosym > > Thanks > Tapas > ************************************************ Piotr K. Wawrzyniak, M.Sc. Solid State NMR Group Leiden Institute of Chemistry, Leiden University P.O. Box 9502, 2300 RA Leiden The Netherlands Phone: +31 71 527 4653 Fax: +31 71 527 4603 e-mail: p.k.wawrzyniak-,-chem.leidenuniv.nl webpage: http://wwwchem.gorlaeus.net/ssnmr/piotr ************************************************ From owner-chemistry@ccl.net Fri Mar 16 09:53:00 2007 From: "Jadhav, Ajit \(NIH/NHGRI\) E ajadhav#%#mail.nih.gov" To: CCL Subject: CCL: program to split sdf file Message-Id: <-33816-070316085808-13407-ZYTHldgG3BcBP2czlrZ18Q(!)server.ccl.net> X-Original-From: "Jadhav, Ajit \(NIH/NHGRI\) [E]" Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C767C6.2C3900CC" Date: Fri, 16 Mar 2007 08:25:24 -0400 MIME-Version: 1.0 Sent to CCL by: "Jadhav, Ajit \(NIH/NHGRI\) [E]" [ajadhav~~mail.nih.gov] This is a multi-part message in MIME format. ------_=_NextPart_001_01C767C6.2C3900CC Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Checkout Manish Sud's free Perl library: http://www.mayachemtools.org/=20 which includes SplitSDFiles.pl, http://www.mayachemtools.org/docs/html/SplitSDFiles.html in which you can specify how many files you want to split the sdf into. =20 --Ajit NIH Chemical Genomics Center =20 ________________________________ > From: Fan,Huajun hjfan^^^pvamu.edu [mailto:owner-chemistry:+:ccl.net]=20 Sent: Friday, March 16, 2007 1:39 AM To: Jadhav, Ajit (NIH/NHGRI) [E] Subject: CCL: program to split sdf file =20 Hi, Does anyone know any programs (preferably free) that can split a big sdf file into smaller files? I got a sdf file containing 30,000 molecules and want to do a DOCK5. It is too big even to read it through. I want to split it into 10 samller files that contains 3,000 each. Is it possible? The newest version of Babel seems not available of this split function for SDF format. =20 Thanks in advance. =20 Hua-Jun=20 =20 ------_=_NextPart_001_01C767C6.2C3900CC Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Checkout Manish Sud’s free = Perl library: http://www.mayachemtools.org/

which includes SplitSDFiles.pl, http://= www.mayachemtools.org/docs/html/SplitSDFiles.html

in which you can specify how many = files you want to split the sdf into.

 

--Ajit

NIH Chemical Genomics Center

 

From: = Fan,Huajun hjfan^^^pvamu.edu [mailto:owner-chemistry:+:ccl.net]
Sent: Friday, March 16, = 2007 1:39 AM
To: Jadhav, Ajit = (NIH/NHGRI) [E]
Subject: CCL: program to = split sdf file

 

Hi, Does anyone know any programs (preferably free) = that can split a big sdf file into smaller files? I got a sdf file containing = 30,000 molecules and want to do a DOCK5. It is too big even to read it through. = I want to split it into 10 samller files that contains 3,000 each. Is it = possible? The newest version of = Babel seems not available of this = split function for SDF format.

 

Thanks in advance.

 

Hua-Jun =

 

------_=_NextPart_001_01C767C6.2C3900CC-- From owner-chemistry@ccl.net Fri Mar 16 10:30:00 2007 From: "Geoffrey Hutchison grh25~~cornell.edu" To: CCL Subject: CCL: program to split sdf file Message-Id: <-33817-070316091422-22183-YJqBPGjX9+9KAv6RN8fKFA::server.ccl.net> X-Original-From: Geoffrey Hutchison Content-Type: multipart/alternative; boundary=Apple-Mail-2-320725816 Date: Fri, 16 Mar 2007 08:42:17 -0400 Mime-Version: 1.0 (Apple Message framework v752.2) Sent to CCL by: Geoffrey Hutchison [grh25[#]cornell.edu] --Apple-Mail-2-320725816 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed Every version of Babel can do this, because you can set the beginning =20= and end records for conversion. babel -f 1 -l 3000 -isdf BIG.sdf -osdf small1.sdf Then repeat! babel -f 3001 -l 6000 -isdf BIG.sdf -osdf small2.sdf babel -f 6001 -l 9000 -isdf BIG.sdf -osdf small3.sdf # etc. If you want a more "automatic" method, it's pretty easy to write a =20 shell script. Otherwise, feel free to report problems (or requests) =20 about Open Babel to us via the SourceForge project page: http://=20 sourceforge.net/projects/openbabel If we don't know of your problems, there's much less chance we'll =20 address them. (In this case, most people splitting large files =20 typically want to split into smaller files of 1 molecule each.) Cheers, -Geoff -- -Dr. Geoffrey Hutchison Cornell University, Department of Chemistry and Chemical Biology Abru=F1a Group http://abruna.chem.cornell.edu/ On Mar 16, 2007, at 1:38 AM, Fan,Huajun hjfan^^^pvamu.edu wrote: > Hi, Does anyone know any programs (preferably free) that can split =20 > a big sdf file into smaller files? I got a sdf file containing =20 > 30,000 molecules and want to do a DOCK5. It is too big even to read =20= > it through. I want to split it into 10 samller files that contains =20 > 3,000 each. Is it possible? The newest version of Babel seems not =20 > available of this split function for SDF format. > > > > Thanks in advance. > > > > Hua-Jun > > > > --Apple-Mail-2-320725816 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 Every version of Babel can do = this, because you can set the beginning and end records for = conversion.

babel = -f 1 -l 3000 -isdf BIG.sdf -osdf small1.sdf

Then repeat!

babel -f 3001 -l 6000 -isdf = BIG.sdf -osdf small2.sdf
babel -f 6001 -l 9000 -isdf BIG.sdf = -osdf small3.sdf
# etc.

If you want a more = "automatic" method, it's pretty easy to write a shell script. Otherwise, = feel free to report problems (or requests) about Open Babel to us via = the SourceForge project page: http://sourceforge.net/= projects/openbabel

If we don't know of your = problems, there's much less chance we'll address them. (In this case, = most people splitting large files typically want to split into smaller = files of 1 molecule each.)

Cheers,
-Geoff
<= DIV>

--
-Dr. Geoffrey Hutchison=A0 =A0 =A0= =A0 <grh25#%#cornell.edu>
=
Cornell University, Department of Chemistry and Chemical = Biology
Abru=F1a Group=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 http://abruna.chem.cornell.edu= /

On Mar 16, 2007, at 1:38 AM, Fan,Huajun = hjfan^^^pvamu.edu wrote:

Hi, Does anyone know any programs (preferably free) that = can split a big sdf file into smaller files? I got a sdf file containing = 30,000 molecules and want to do a DOCK5. It is too big even to read it = through. I want to split it into 10 samller files that contains 3,000 = each. Is it possible? The newest version of = Babel seems not available of this split = function for SDF format.

=A0

Thanks in advance.=A0


= --Apple-Mail-2-320725816-- From owner-chemistry@ccl.net Fri Mar 16 11:03:00 2007 From: "Dan Maftei dan.maftei~!~chem.uaic.ro" To: CCL Subject: CCL: GULP failure in NPT molecular dynamics Message-Id: <-33818-070316095943-21446-yDgS9mZjHVKqnOFjb4M0/Q[-]server.ccl.net> X-Original-From: Dan Maftei Content-Type: multipart/mixed; boundary="------------040105050309060301010606" Date: Fri, 16 Mar 2007 15:57:14 +0200 MIME-Version: 1.0 Sent to CCL by: Dan Maftei [dan.maftei]|[chem.uaic.ro] This is a multi-part message in MIME format. --------------040105050309060301010606 Content-Type: text/plain; charset=ISO-8859-2; format=flowed Content-Transfer-Encoding: 7bit Dear CCL-ers, I use GULP to perform NPT molecular dynamics simulations on some perovskite-like structures. The Buckingham potential model parameters used (Catlow & Lewis) were able to reproduce the observed (XRD) crystal structure. The MD simulations run well at different temperatures below 250K. Failures were encountered at lower temperatures ("unphysical cell dimensions", "too many lattice vectors..."), mainly as a result of temperature "instabilities" in the production runs. Is there a way to control the thermostat parameters in GULP? Thank you in advance, Dan Maftei --------------040105050309060301010606 Content-Type: text/x-vcard; charset=utf-8; name="dan.maftei.vcf" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="dan.maftei.vcf" begin:vcard fn:Dan Maftei n:Maftei;Dan org:"Alexandru Ioan Cuza" University;Physical, Theoretical and Materials Chemistry adr:Nr. 11;;Bd. Carol 1, ;Iasi;;700506;Romania email;internet:dan.maftei],[chem.uaic.ro title:Faculty of Chemistry tel;work:+40232-201307 tel;cell:+40740-262227 x-mozilla-html:FALSE url:http://www.chem.uaic.ro/~danmaftei version:2.1 end:vcard --------------040105050309060301010606-- From owner-chemistry@ccl.net Fri Mar 16 11:41:00 2007 From: "Anselm.Horn*o*chemie.uni-erlangen.de" To: CCL Subject: CCL: program to split sdf file Message-Id: <-33819-070316061033-5962-PfZ1xEZNe/RXbdly124K3w]![server.ccl.net> X-Original-From: Anselm.Horn/./chemie.uni-erlangen.de Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Fri, 16 Mar 2007 10:03:45 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: Anselm.Horn . chemie.uni-erlangen.de Hi Hua-Jun, > Hi, Does anyone know any programs (preferably free) that can split a big > sdf file into smaller files? I got a sdf file containing 30,000 > molecules and want to do a DOCK5. It is too big even to read it through. > I want to split it into 10 samller files that contains 3,000 each. Is it > possible? The newest version of Babel seems not available of this split > function for SDF format. have a look at http://www.mayachemtools.org, where a perl-script SplitSDFiles.pl is available, that probably does what you want. Regards, Anselm From owner-chemistry@ccl.net Fri Mar 16 12:13:01 2007 From: "Pankaj R. Daga pdaga- -olemiss.edu" To: CCL Subject: CCL: program to split sdf file Message-Id: <-33820-070316102045-2151-aoybm8YKoraG/1IlD8zxMA###server.ccl.net> X-Original-From: "Pankaj R. Daga" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0015_01C767A7.BB0980B0" Date: Fri, 16 Mar 2007 08:47:29 -0500 MIME-Version: 1.0 Sent to CCL by: "Pankaj R. Daga" [pdaga]![olemiss.edu] This is a multi-part message in MIME format. ------=_NextPart_000_0015_01C767A7.BB0980B0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hey Hua-Jun If you have access to Perl, there are very good tools available from = "MAYACHEMTOOLS". =20 MayaChemTools is a collection of command line Perl scripts to work with = SD files, CSV/TSV text files, Sequence/Alignments files, PDB files, and = databases: splitting, joining, merging, and sorting SD and text files; = merging text files into SD files; splitting SD files into MDL MOL files; = generating HTML files from SD and text files; calculating descriptive = statistics for numerical data in SD and text files; exporting data from = MySQL and Oracle tables into text files; perform elemental analysis = using formula information in SD and text files; extracting data from PDB = and Sequence/Alignment files; modifying PDB files; analyzing = Sequence/Alignment file; and so on. Hope this helps PanDa =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 If your ship doesn't come in, swim out to it.......Jonathan Winters =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 Pankaj R. Daga | =20 Department of Medicinal Chemistry | e-mail: pdaga_at_olemiss.edu 417 Faser Hall, School of Pharmacy | fax: +1-662-915-5638 University of Mississippi | phone: +1-662-915-1853 University, MS, 38677-1848 | =20 =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 ----- Original Message -----=20 > From: Fan,Huajun hjfan^^^pvamu.edu=20 To: Daga, Pankaj R =20 Sent: Friday, March 16, 2007 12:38 AM Subject: CCL: program to split sdf file Hi, Does anyone know any programs (preferably free) that can split a big = sdf file into smaller files? I got a sdf file containing 30,000 = molecules and want to do a DOCK5. It is too big even to read it through. = I want to split it into 10 samller files that contains 3,000 each. Is it = possible? The newest version of Babel seems not available of this split = function for SDF format. =20 Thanks in advance. =20 Hua-Jun=20 ------=_NextPart_000_0015_01C767A7.BB0980B0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hey=20 Hua-Jun
 
If = you have=20 access to Perl, there are very good tools available from=20 "MAYACHEMTOOLS". 
 
MayaChemTools=20 is a collection of command line Perl scripts to work with SD files, = CSV/TSV text=20 files, Sequence/Alignments files, PDB files, and databases: splitting, = joining,=20 merging, and sorting SD and text files; merging text files into SD = files;=20 splitting SD files into MDL MOL files; generating HTML files from SD and = text=20 files; calculating descriptive statistics for numerical data in SD and = text=20 files; exporting data from MySQL and Oracle tables into text files; = perform=20 elemental analysis using formula information in SD and text files; = extracting=20 data from PDB and Sequence/Alignment files; modifying PDB files; = analyzing=20 Sequence/Alignment file; and so on.
 
Hope = this=20 helps
 
PanDa
 

=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
If=20 your ship doesn't come in, swim out to it.......Jonathan=20 Winters
=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
Pankaj= =20 R.=20 Daga           &nb= sp;        =20 | 
Department of Medicinal Chemistry  |  = e-mail: =20 pdaga_at_olemiss.edu
417 Faser Hall, School of Pharmacy | =20 fax:         =20 +1-662-915-5638
University of=20 Mississippi          = | =20 phone:        = +1-662-915-1853
University,=20 MS, 38677-1848         | =20
=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
-----=20 Original Message -----
From: Fan,Huajun hjfan^^^pvamu.edu
To: = Daga,=20 Pankaj R
Sent: Friday, March 16, 2007 12:38 AM
Subject: = CCL:=20 program to split sdf file


Hi, Does anyone know any programs=20 (preferably free) that can split a big sdf file into smaller files? I = got a sdf=20 file containing 30,000 molecules and want to do a DOCK5. It is too big = even to=20 read it through. I want to split it into 10 samller files that contains = 3,000=20 each. Is it possible? The newest version of Babel seems not available of = this=20 split function for SDF format.
 
Thanks in=20 advance.
 
Hua-Jun
 
------=_NextPart_000_0015_01C767A7.BB0980B0-- From owner-chemistry@ccl.net Fri Mar 16 12:47:01 2007 From: "Gopakumar gopakumar+*+chem.kuleuven.be" To: CCL Subject: CCL: Centroid of a Molecule Message-Id: <-33821-070316113211-21736-Q1QY/E7gpHW5oeWuhqNlKw()server.ccl.net> X-Original-From: Gopakumar Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Fri, 16 Mar 2007 16:31:55 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: Gopakumar [gopakumar_-_chem.kuleuven.be] Does anybody know a program to determine the centroid of a molecule (eg. cages)... Is there any free program available for this purpose... any help is much appreciated. thanks -Gopakumar __________________________________________________________ G. Gopakumar, Division of Quantum Chemistry and Physical Chemistry, Department of Chemistry, University of Leuven, Celestijnenlaan 200F, B-3001 Heverlee (Leuven), Belgium. e-mail: gopakumar(~)chem.kuleuven.be Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm From owner-chemistry@ccl.net Fri Mar 16 13:23:00 2007 From: "graham.mullier+*+syngenta.com" To: CCL Subject: CCL: program to split sdf file Message-Id: <-33822-070316074041-13416-XvwQ2mQAD8Mtcp9Dhe9uww(0)server.ccl.net> X-Original-From: Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C767B7.7EC5F16B" Date: Fri, 16 Mar 2007 10:40:20 -0000 MIME-Version: 1.0 Sent to CCL by: [graham.mullier|a|syngenta.com] This is a multi-part message in MIME format. ------_=_NextPart_001_01C767B7.7EC5F16B Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable at the risk of sounding like someone who sees all SDF-manipulation problems as nails to be hit with a hammer (awk), you could use an awk script... =20 assuming you want to split, as you say, into 3000-member chunks, something like =20 BEGIN { prefix =3D "fred" suffix =3D ".sdf" block =3D 1 outf =3D prefix block suffix } =20 # write lines to named output file {print $0 >outf} =20 #count number of molecules $1 =3D=3D "$$$$" {nmol++} =20 #and flip to next block/output file after limit, 3000 in this case nmol >=3D 3000 { close (outf) block++ outf =3D prefix block suffix nmol =3D 0 } should work (though you might like to test it yourself... I haven't). If it's in a file called 'splitsdf.awk' then =20 awk -f splitsdf.awk largefile.sdf =20 should do the trick, producing fred1.sdf, fred2.sdf etc. =20 Other scripting languages are available. Language popularities can go down as well as up. Your mileage may vary. =20 Graham ________________________________ From: owner-chemistry|-|ccl.net [mailto:owner-chemistry|-|ccl.net]=20 Sent: Fri 16 March 2007 05:39 To: Mullier Graham GBJH Subject: CCL: program to split sdf file =09 =09 Hi, Does anyone know any programs (preferably free) that can split a big sdf file into smaller files? I got a sdf file containing 30,000 molecules and want to do a DOCK5. It is too big even to read it through. I want to split it into 10 samller files that contains 3,000 each. Is it possible? The newest version of Babel seems not available of this split function for SDF format. =20 Thanks in advance. =20 Hua-Jun=20 =20 ------_=_NextPart_001_01C767B7.7EC5F16B Content-Type: text/html; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable
at the risk of sounding like someone who sees = all=20 SDF-manipulation problems as nails to be hit with a hammer (awk), you = could use=20 an awk script...
 
assuming you want to split, as you say, into = 3000-member=20 chunks, something like
 
BEGIN
{ prefix =3D "fred"
  suffix =3D ".sdf"
  block =3D 1
  outf =3D prefix block = suffix
}
 
# write lines to named output = file
{print $0 >outf}
 
#count number of molecules
$1 =3D=3D "$$$$" {nmol++}
 
#and flip to next block/output file after = limit, 3000 in=20 this case
nmol >=3D 3000=20 {
    close=20 (outf)
   =20 block++
    outf =3D prefix block=20 suffix
    nmol =3D 0
}
should=20 work (though you might like to test it yourself... I haven't). If it's = in a file=20 called 'splitsdf.awk' then
 
awk -f=20 splitsdf.awk largefile.sdf
 
should=20 do the trick, producing fred1.sdf, fred2.sdf etc.
 
Other=20 scripting languages are available. Language popularities can go down as = well as=20 up. Your mileage may vary.
 
Graham
From: owner-chemistry|-|ccl.net=20 [mailto:owner-chemistry|-|ccl.net]
Sent: Fri 16 March 2007=20 05:39
To: Mullier Graham GBJH
Subject: CCL: = program to=20 split sdf file

Hi, Does anyone know any = programs=20 (preferably free) that can split a big sdf file into smaller files? I = got a=20 sdf file containing 30,000 molecules and want to do a DOCK5. It is too = big=20 even to read it through. I want to split it into 10 samller files that = contains 3,000 each. Is it possible? The newest version of Babel seems not available of this = split=20 function for SDF format.

 

Thanks in=20 advance.

 

Hua-Jun=20

 

------_=_NextPart_001_01C767B7.7EC5F16B-- From owner-chemistry@ccl.net Fri Mar 16 13:57:00 2007 From: "Michel Petitjean ptitjean,+,itodys.jussieu.fr" To: CCL Subject: CCL: Centroid of a Molecule Message-Id: <-33823-070316133422-15136-ffvouW64MN7TXm0qGrrflA,server.ccl.net> X-Original-From: Michel Petitjean Date: Fri, 16 Mar 2007 18:33:56 +0100 (MET) Sent to CCL by: Michel Petitjean [ptitjean[A]itodys.jussieu.fr] To: chemistry-#-ccl.net Subject: CCL: Re: Centroid of a Molecule RADI does that, among other things: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#RADI Michel Petitjean, Email: petitjean-#-itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean-#-ccr.jussieu.fr 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.html Sent to CCL by: Gopakumar [gopakumar_-_chem.kuleuven.be] > Does anybody know a program to determine the centroid of a molecule (eg. > cages)... Is there any free program available for this purpose... any help > is much appreciated. > > thanks > > -Gopakumar > __________________________________________________________ > G. Gopakumar, > Division of Quantum Chemistry and Physical Chemistry, > Department of Chemistry, University of Leuven, > Celestijnenlaan 200F, B-3001 Heverlee (Leuven), Belgium. > e-mail: gopakumar(-)chem.kuleuven.be > > >Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm From owner-chemistry@ccl.net Fri Mar 16 14:48:00 2007 From: "Dipesh Risal drisal]![accelrys.com" To: CCL Subject: CCL: Centroid of a Molecule Message-Id: <-33824-070316142126-15980-98BATifLAWO6+3brC2uz7g\a/server.ccl.net> X-Original-From: Dipesh Risal Content-Type: multipart/alternative; boundary="=_alternative 00620114882572A0_=" Date: Fri, 16 Mar 2007 10:50:31 -0700 MIME-Version: 1.0 Sent to CCL by: Dipesh Risal [drisal|a|accelrys.com] This is a multipart message in MIME format. --=_alternative 00620114882572A0_= Content-Type: text/plain; charset="US-ASCII" Hi, Discovery Studio Visualizer (free for everyone) can do this. Select molecule/atoms of interest, and then Structure > Monitor > Centroid http://www.accelrys.com/products/downloads/ds_visualizer/ Best, Dipesh Risal, Ph. D. Product Manager, Life Sciences Accelrys, Inc. 10188 Telesis Court, Suite 100 San Diego, CA 92121, U.S.A. Tel: +1 (858) 799 5224, Cell: +1 (858) 414 2702 Fax: +1 (858) 799 5100 email: drisal]![accelrys.com http://www.accelrys.com "Gopakumar gopakumar+*+chem.kuleuven.be" Sent by: owner-chemistry]![ccl.net 03/16/2007 08:31 AM Please respond to "CCL Subscribers" To "Risal, Dipesh " cc Subject CCL: Centroid of a Molecule Sent to CCL by: Gopakumar [gopakumar_-_chem.kuleuven.be] Does anybody know a program to determine the centroid of a molecule (eg. cages)... Is there any free program available for this purpose... any help is much appreciated. thanks -Gopakumar __________________________________________________________ G. Gopakumar, Division of Quantum Chemistry and Physical Chemistry, Department of Chemistry, University of Leuven, Celestijnenlaan 200F, B-3001 Heverlee (Leuven), Belgium. e-mail: gopakumar(-)chem.kuleuven.be Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htmhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt-- Click on the link below to report this email as spam https://www.mailcontrol.com/sr/WfRySkjceR3CX5HwtzsSjnnlrwbl!z9m0iLRKAbll08b2WahpCZyVlKUPlgQ8vrg6e95a3rZgR1bDHAp893k5RHTS!tD!eIBs0uoYXqFGK02w!z3yHnLxq51fbhBgAmMG4Pgy5hKQ41HlUhseFtlWOoKDd!v!671D7M!rBGhZrCfWXuJfWfjFSFBJe9ib8A!sFK8qQJgVZ!WfQof2okvdIFyEpEHQoQr --=_alternative 00620114882572A0_= Content-Type: text/html; charset="US-ASCII"

Hi,

Discovery Studio Visualizer (free for everyone) can do this.

Select molecule/atoms of interest,  and then Structure > Monitor > Centroid

http://www.accelrys.com/products/downloads/ds_visualizer/

Best,

Dipesh Risal, Ph. D.
Product Manager, Life Sciences
Accelrys, Inc.
10188 Telesis Court, Suite 100
San Diego, CA 92121, U.S.A.
Tel:  +1 (858) 799 5224, Cell:  +1 (858) 414 2702
Fax: +1 (858) 799 5100
email: drisal]![accelrys.com
http://www.accelrys.com


"Gopakumar gopakumar+*+chem.kuleuven.be" <owner-chemistry]![ccl.net>
Sent by: owner-chemistry]![ccl.net

03/16/2007 08:31 AM
Please respond to
"CCL Subscribers" <chemistry]![ccl.net>
To
"Risal, Dipesh " <drisal]![accelrys.com>
cc
Subject
CCL: Centroid of a Molecule






Sent to CCL by: Gopakumar [gopakumar_-_chem.kuleuven.be]
Does anybody know a program to determine the centroid of a molecule (eg.
cages)... Is there any free program available for this purpose... any help
is much appreciated.

thanks

-Gopakumar
__________________________________________________________
G. Gopakumar,                                                              
Division of Quantum Chemistry and Physical Chemistry,
Department of Chemistry, University of Leuven,
Celestijnenlaan  200F, B-3001 Heverlee (Leuven), Belgium.
e-mail: gopakumar(-)chem.kuleuven.be  


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--=_alternative 00620114882572A0_=-- From owner-chemistry@ccl.net Fri Mar 16 15:22:01 2007 From: "Martin Lindh martinlindh{=}yahoo.se" To: CCL Subject: CCL: Babel problem (?) Message-Id: <-33825-070316131617-32127-ELjJR76Jei49Qp0WTL0ytw . server.ccl.net> X-Original-From: "Martin Lindh" Date: Fri, 16 Mar 2007 13:16:13 -0400 Sent to CCL by: "Martin Lindh" [martinlindh-$-yahoo.se] Hi I prepare ligands using LigPrep (Maestro). Since I want to dock these ligands in FlexX (Sybyl), I export the ligands from Maestro as a .sdf file. I then use Babel to convert the .sdf file to a multi .mol2 file. The .mol2 file is then imported into Sybyl. During this process some(!) of the ligands get strange mol2 formating. Part of a molecule that is translated correctly into the mol2-file: () ATOM 1 P1 -7.7746 0.3497 0.1484 P.3 1 <1> 0.1085 2 O1 -7.2207 1.7666 -0.1209 O.2 1 <1> -0.4607 3 O2 -7.9571 -0.5515 -1.0931 O.co2 1 <1> -0.3575 Part of a molecule that is NOT translated correctly in mol2-file: 28 C 14.2736 6.1106 -1.8492 C.ar 0 UNK0 0.1493 29 N 14.3973 5.3090 -0.7250 N.ar 0 UNK0 -0.2079 30 N 13.7198 8.3248 -1.0353 N.pl3 0 UNK0 -0.3413 31 C1* 15.1231 2.8403 -3.4280 C.3 1 UNK1 0.1683 32 O4* 15.0326 3.1353 -4.7858 O.3 1 UNK1 -0.3456 33 C4* 13.7316 2.8114 -5.2536 C.3 1 UNK1 0.1126 Anyone seen this problem and have suggestions of what to do? Thank you in advance Martin From owner-chemistry@ccl.net Fri Mar 16 17:41:00 2007 From: "latha plmallip^^mail.uh.edu" To: CCL Subject: CCL: program to split sdf file Message-Id: <-33826-070316105218-25859-Yxe8yhqMaVjTJStLIrmSSw^server.ccl.net> X-Original-From: latha Content-type: multipart/alternative; boundary="Boundary_(ID_FHQkVsAC0xrWUZoxTUezEw)" Date: Fri, 16 Mar 2007 09:53:54 -0500 MIME-version: 1.0 Sent to CCL by: latha [plmallip###mail.uh.edu] This is a multi-part message in MIME format. --Boundary_(ID_FHQkVsAC0xrWUZoxTUezEw) Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: QUOTED-PRINTABLE You can also try "hjsplit". Its free. But you need to edit the last m= olecule, it will be splitted in two files. warm regards, Latha. ----- Original Message -----=20 From: Mads N=F8rregaard-Madsen MN.!^!.nuevolution.com=20 To: Mallipeddi, Prema Latha =20 Sent: Friday, March 16, 2007 2:52 AM Subject: CCL: program to split sdf file Hi, =20 You could try ChemFileBrowser - www.hyleos.net =20 /Mads =20 ---------------------------------------------------------------------= --------- From: owner-chemistry . ccl.net [mailto:owner-chemistry . ccl.net]= =20 Sent: Friday, March 16, 2007 6:39 AM To: Mads N=F8rregaard-Madsen Subject: CCL: program to split sdf file =20 Hi, Does anyone know any programs (preferably free) that can split = a big sdf file into smaller files? I got a sdf file containing 30,000= molecules and want to do a DOCK5. It is too big even to read it thro= ugh. I want to split it into 10 samller files that contains 3,000 eac= h. Is it possible? The newest version of Babel seems not available of= this split function for SDF format. =20 Thanks in advance. =20 Hua-Jun=20 =20 --Boundary_(ID_FHQkVsAC0xrWUZoxTUezEw) Content-type: text/html; charset=iso-8859-1 Content-transfer-encoding: QUOTED-PRINTABLE
You can also try "hjsplit". Its free= . But you=20 need to edit the last molecule, it will be splitted in two files.
 
warm regards,
Latha.
----- Original Message -----
= From:=20 Mads=20 N=F8rregaard-Madsen MN.!^!.nuevolution.com
Sent: Friday, March 16, 2007= 2:52=20 AM
Subject: CCL: program to spl= it sdf=20 file

Hi,=

&nb= sp;

You coul= d try=20 ChemFileBrowser =96 www.hyleos.net

&nb= sp;

/Mads

&nb= sp;

=

F= rom: owner-chemistry . c= cl.net=20 [mailto:owner-chemistry . ccl.net]
Sent: Friday, March 16, 2007= 6:39=20 AM
To: Mads N=F8rregaard-Madsen
Subject: CCL: program to spl= it sdf=20 file

 

Hi, Does anyone know = any programs=20 (preferably free) that can split a big sdf file into smaller files?= I got a=20 sdf file containing 30,000 molecules and want to do a DOCK5. It is = too big=20 even to read it through. I want to split it into 10 samller files t= hat=20 contains 3,000 each. Is it possible? The newest version of Babel seems not available of thi= s split=20 function for SDF format.

 

Thanks in=20 advance.

 

Hua-Jun=20

 

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