From owner-chemistry@ccl.net Wed Feb 21 00:01:00 2007 From: "Ben Vastine vastinator]-[gmail.com" To: CCL Subject: CCL: the cases which B3LYP method or 6-31+G** basis set overestimates Message-Id: <-33666-070220141417-16667-ywyS3C5lFBFDbtqcN2PB8w\a/server.ccl.net> X-Original-From: "Ben Vastine" Content-Type: multipart/alternative; boundary="----=_Part_60563_3273196.1171992136041" Date: Tue, 20 Feb 2007 11:22:16 -0600 MIME-Version: 1.0 Sent to CCL by: "Ben Vastine" [vastinator,+,gmail.com] ------=_Part_60563_3273196.1171992136041 Content-Type: text/plain; charset=ISO-8859-2; format=flowed Content-Transfer-Encoding: base64 Content-Disposition: inline SWYgdGhpcyByZWFjdGlvbiBpbnZvbHZlcyBoeWRyb2dlbiB0cmFuc2ZlciwgdGhlbiBoeWRyb2dl biB0dW5uZWxpbmcgbWF5IGJlCmltcG9ydGFudC4gIFRoZXJlIGFyZSB0cmFuc2l0aW9uIHN0YXRl IHRoZW9yeSBjb3JyZWN0aW9ucyBmb3IgaHlkcm9nZW4KdHVubmVsaW5nLCBhbmQgdGhlc2UgbWF5 IGhlbHAgZXhwbGFpbiB0aGUgYmFycmllciB0aGF0IHlvdSBhcmUgY2FsY3VsYXRpbmcuCgpCZW4K CgoKT24gMi8yMC8wNywgR9xMIEFMVElOQkGqIGdhbHRpbmJhcyBfIGdtYWlsLmNvbSA8b3duZXIt Y2hlbWlzdHJ5QGNjbC5uZXQ+Cndyb3RlOgo+Cj4gSGkgYWxsLAo+IEkgaGF2ZSBiZWVuIHN0dWR5 aW5nIG9uIHRoZSBtZWNoYW5pc20gb2YgYW4gb3JnYW5pYyByZWFjdGlvbiB3aGljaCAgb2NjdXJz Cj4gYXQgcm9vbSB0ZW1wZXJhdHVyZS4gSSBhbSB1c2luZyBCM0xZUC82LTMxK0cqKiBiYXNpcyBz ZXQgc2luY2Ugb3VyCj4gc3RydWN0dXJlcyBhcmUgY2hhcmdlZC4gV2UgcHJvcG9zZWQgdHdvIHBs YXVzaWJsZSBtZWNoYW5pc21zLiAgSSBmb3VuZCB0aGUKPiBhY3RpdmF0aW9uIGJhcnJpZXJzIG9m IHRoZSByYXRlIGRldGVybWluaW5nIHN0ZXBzIG9mIHRoZXNlIG1lY2hhbmlzbXMgYXMgNDUKPiBh bmQgNTggIGtjYWwvbW9sZS4gVGhlc2UgZW5lcmd5IGFyZSAgdG9vIGhpZ2ggZm9yIHRoZSByZWFj dGlvbiBhdCByb29tCj4gdGVtcGVyYXR1cmUuIE15IHF1ZXN0aW9uIGlzOgo+ICJEb2VzIGFueW9u ZSBrbm93IGEgc3BlY2lhbCBjYXNlIGluIHdoaWNoIEIzTFlQIG1ldGhvZCBvciA2LTMxK0coZCxw KQo+IGJhc2lzIHNldCBvdmVyZXN0aW1hdGVzIHRoZSBhY3RpdmF0aW9uIGJhcnJpZXI/Igo+IEkg YW0gd2FpdGluZyBmb3IgeW91ciBhbnN3ZXJzIG9yIGFueSBzdWdnZXN0aW9ucy4KPiBCZXN0IHJl Z2FyZHMKPiBHdWwKPiAtLQo+IEf8bCBBbHRpbmJhcyBPenBpbmFyCj4gUmVzZWFyY2ggQXNzaXN0 YW50Cj4gTWFybWFyYSBVbml2ZXJzaXR5Cj4gQXJ0cyZTY2llbmNlcyBGYWN1bHR5Cj4gQ2hlbWlz dHJ5IERlcGFydG1lbnQKPiBH9np0ZXBlIENhbXB1cyAzNDcyMgo+IElzdGFuYnVsIC8gVHVya2V5 Cj4gUGhvbmUgTm86ICs5MCAyMTYgMzQ3IDk2IDQxIC0gMTE2Nwo+IEZheCBObzogKyA5MCAyMTYg MzQ3IDg3IDgzCg== ------=_Part_60563_3273196.1171992136041 Content-Type: text/html; charset=ISO-8859-2 Content-Transfer-Encoding: base64 Content-Disposition: inline SWYgdGhpcyByZWFjdGlvbiBpbnZvbHZlcyBoeWRyb2dlbiB0cmFuc2ZlciwgdGhlbiBoeWRyb2dl biB0dW5uZWxpbmcgbWF5IGJlIGltcG9ydGFudC4mbmJzcDsgVGhlcmUgYXJlIHRyYW5zaXRpb24g c3RhdGUgdGhlb3J5IGNvcnJlY3Rpb25zIGZvciBoeWRyb2dlbiB0dW5uZWxpbmcsIGFuZCB0aGVz ZSBtYXkgaGVscCBleHBsYWluIHRoZSBiYXJyaWVyIHRoYXQgeW91IGFyZSBjYWxjdWxhdGluZy4K PGJyPjxicj5CZW48YnI+PGJyPjxicj48YnI+PGRpdj48c3BhbiBjbGFzcz0iZ21haWxfcXVvdGUi Pk9uIDIvMjAvMDcsIDxiIGNsYXNzPSJnbWFpbF9zZW5kZXJuYW1lIj5H3EwgQUxUSU5CQaogZ2Fs dGluYmFzIF8gPGEgaHJlZj0iaHR0cDovL2dtYWlsLmNvbSI+Z21haWwuY29tPC9hPjwvYj4gJmx0 OzxhIGhyZWY9Im1haWx0bzpvd25lci1jaGVtaXN0cnlAY2NsLm5ldCI+b3duZXItY2hlbWlzdHJ5 QGNjbC5uZXQKPC9hPiZndDsgd3JvdGU6PC9zcGFuPjxibG9ja3F1b3RlIGNsYXNzPSJnbWFpbF9x dW90ZSIgc3R5bGU9ImJvcmRlci1sZWZ0OiAxcHggc29saWQgcmdiKDIwNCwgMjA0LCAyMDQpOyBt YXJnaW46IDBwdCAwcHQgMHB0IDAuOGV4OyBwYWRkaW5nLWxlZnQ6IDFleDsiPkhpIGFsbCw8YnI+ CkkgaGF2ZSBiZWVuIHN0dWR5aW5nIG9uIHRoZSBtZWNoYW5pc20gb2YgYW4gb3JnYW5pYyByZWFj dGlvbgp3aGljaCZuYnNwOyBvY2N1cnMgYXQgcm9vbSB0ZW1wZXJhdHVyZS4gSSBhbSB1c2luZyBC M0xZUC82LTMxK0cqKiBiYXNpcwpzZXQgc2luY2Ugb3VyIHN0cnVjdHVyZXMgYXJlIGNoYXJnZWQu IFdlIHByb3Bvc2VkIHR3byBwbGF1c2libGUKbWVjaGFuaXNtcy4mbmJzcDsgSSBmb3VuZCB0aGUg YWN0aXZhdGlvbiBiYXJyaWVycyBvZiB0aGUgcmF0ZQpkZXRlcm1pbmluZyBzdGVwcyBvZiB0aGVz ZSBtZWNoYW5pc21zIGFzIDQ1IGFuZCA1OCZuYnNwOyBrY2FsL21vbGUuClRoZXNlIGVuZXJneSBh cmUmbmJzcDsgdG9vIGhpZ2ggZm9yIHRoZSByZWFjdGlvbiBhdCByb29tIHRlbXBlcmF0dXJlLgpN eSBxdWVzdGlvbiBpczo8YnI+CiZxdW90O0RvZXMgYW55b25lIGtub3cgYSBzcGVjaWFsIGNhc2Ug aW4gd2hpY2ggQjNMWVAgbWV0aG9kIG9yIDYtMzErRyhkLHApIGJhc2lzIHNldCBvdmVyZXN0aW1h dGVzIHRoZSBhY3RpdmF0aW9uIGJhcnJpZXI/JnF1b3Q7IDxicj4KSSBhbSB3YWl0aW5nIGZvciB5 b3VyIGFuc3dlcnMgb3IgYW55IHN1Z2dlc3Rpb25zLjxicj4KQmVzdCByZWdhcmRzPGJyPgpHdWw8 YnI+LS0gPGJyPkf8bCBBbHRpbmJhcyBPenBpbmFyPGJyPlJlc2VhcmNoIEFzc2lzdGFudDxicj5N YXJtYXJhIFVuaXZlcnNpdHk8YnI+QXJ0cyZhbXA7U2NpZW5jZXMgRmFjdWx0eSA8YnI+Q2hlbWlz dHJ5IERlcGFydG1lbnQ8YnI+R/Z6dGVwZSBDYW1wdXMgMzQ3MjIgPGJyPklzdGFuYnVsIC8gVHVy a2V5PGJyPlBob25lIE5vOiArOTAgMjE2IDM0NyA5NiA0MSAtIDExNjc8YnI+CgpGYXggTm86ICsg OTAgMjE2IDM0NyA4NyA4Mwo8L2Jsb2NrcXVvdGU+PC9kaXY+PGJyPgo= ------=_Part_60563_3273196.1171992136041-- From owner-chemistry@ccl.net Wed Feb 21 00:35:00 2007 From: "Jim Harrison jim456harrison*_*yahoo.com" To: CCL Subject: CCL:G: an error in terms of frequency calculation in Gaussian 03. Message-Id: <-33667-070221000825-968-0QggVih4A0A3ONbozeSTCg.@.server.ccl.net> X-Original-From: Jim Harrison Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-302071769-1172034486=:36446" Date: Tue, 20 Feb 2007 21:08:06 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Jim Harrison [jim456harrison]~[yahoo.com] --0-302071769-1172034486=:36446 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dr Takumi You have not specify the molecule and its input job. I can only guess the source of the problem. However if I assume that you have perform an optimization and then a frequency job, there a possibility that the initial structure that you have specified in the input is incorrect. As specified in the output "molecule is non-linear". If you have taken a linear structure, remove all symmetry on the molecule and perform an optimization and then a frequency calculation.This lead to an optimized structure of the molecules and then frequency will be computed for this optimized structure. Now if the molecule is very large, it is possible that optimization did not occur [you can check this by looking for four "yes" in the output . if you find four "yes" then the structure has optimized]. If you do not find the four "yes" then the job had stopped due to running out of Step. The solution is to increase the step by using the keyword Maxcycle=100. If you want to restart with the previous job, use the keyword opt (maxcycle=100,restart) freq. normally when this situation of "out of step" occur, the calculation has to proceed automatically proceed to frequency calculation but for the non-optimized structure. It is always good to optimize before performing a frequency calculation. now if the specified molecule is linear and you have impose symmetry at the start of the calculation, the molecule has converge to a linear structure and the calculation had crashed giving errors. Hence the optimized structure of the molecule is a linear structure. Perform the opt and freq job for the linear structure I hope that the above will help you. if this does not help, send an email to help**gaussian.com. They will sort out your problems. Bye Jim "Takumi Hori thori3jp*_*mac.com" wrote: Sent to CCL by: Takumi Hori [thori3jp!=!mac.com] Dear CCL users, I got a following error in terms of frequency calculation in Gaussian03. > (Enter /opt/g03nscco64/g03/l716.exe) > Dipole =-5.74843628D-01-5.82225009D-01 2.70383092D-01 > Polarizability= 6.07153970D+02-3.92605031D+01 5.30253486D+02 > -6.00698286D+01-1.82463985D+01 2.60811735D+02 > Full mass-weighted force constant matrix: > Low frequencies --- Infinity NaN NaN NaN > NaN NaN > Low frequencies --- NaN NaN NaN > Molecule is non-linear but NTrRo=0. > Error termination via Lnk1e in /opt/g03nscco64/g03/l716.exe at Fri > Feb 16 13:04:48 2007. > Job cpu time: 3 days 15 hours 28 minutes 16.0 seconds. > File lengths (MBytes): RWF= 4756 Int= 0 D2E= 0 > Chk= 21 Scr= 1 > Could you please tell me possible reasons why gaussian gave such an error? Could anyone tell me how to fix this problem? Any suggestions are appreciated. Thank you very much in advance for your advice. Best regards, Takumi -- Dr. Takumi Hori Research & Development Laboratories Nippon Steel Chemical Co., Lid. 46-80 Nakabaru Sakinohama Tobata-ku, Kitakyushu, Fukuoka 804-8503 Japan Tel: +81-93-884-1621 Fax: +81-93-884-1923 E-mail: horitk---nscc.co.jp thori3jp---mac.com http://www.nscc.co.jp/english/index.htmlhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--------------------------------- Now that's room service! Choose from over 150,000 hotels in 45,000 destinations on Yahoo! Travel to find your fit. --0-302071769-1172034486=:36446 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dr Takumi

You have not specify the molecule and its input job. I can only guess the source of the problem.  However if I assume that you have perform an optimization and then a frequency job, there a possibility that the initial structure that you have specified in the input  is incorrect. As specified in the output "molecule is non-linear". If you have taken a linear structure, remove all symmetry on the molecule and perform an optimization and then a frequency calculation.This lead to an optimized structure of the molecules and then frequency will be computed for this  optimized structure.
Now if the molecule is very large, it is possible that  optimization did not occur [you can check this by looking for four "yes" in the output . if you find four "yes" then the structure has optimized]. If you do not find the four "yes" then the job had stopped due to running out of Step. The  solution is to increase the step by using the keyword  Maxcycle=100. If you want to restart with the previous job, use the keyword  opt (maxcycle=100,restart)  freq.
normally when this situation of "out of step" occur, the calculation has to proceed automatically proceed to frequency calculation but for the non-optimized structure. It is always good to optimize before performing a frequency calculation.
now if the specified molecule is linear and you have impose symmetry at the start of the calculation, the molecule has converge to a linear structure and the calculation had crashed giving errors. Hence the optimized structure of the molecule is a linear structure. Perform the opt and freq job for the linear structure

I hope that the above will help you. if this does not help, send an email to help**gaussian.com. They will sort out your problems. Bye

Jim


"Takumi Hori thori3jp*_*mac.com" <owner-chemistry**ccl.net> wrote:

Sent to CCL by: Takumi Hori [thori3jp!=!mac.com]
Dear CCL users,

I got a following error in terms of frequency calculation in Gaussian03.

> (Enter /opt/g03nscco64/g03/l716.exe)
> Dipole =-5.74843628D-01-5.82225009D-01 2.70383092D-01
> Polarizability= 6.07153970D+02-3.92605031D+01 5.30253486D+02
> -6.00698286D+01-1.82463985D+01 2.60811735D+02
> Full mass-weighted force constant matrix:
> Low frequencies --- Infinity NaN NaN NaN
> NaN NaN
> Low frequencies --- NaN NaN NaN
> Molecule is non-linear but NTrRo=0.
> Error termination via Lnk1e in /opt/g03nscco64/g03/l716.exe at Fri
> Feb 16 13:04:48 2007.
> Job cpu time: 3 days 15 hours 28 minutes 16.0 seconds.
> File lengths (MBytes): RWF= 4756 Int= 0 D2E= 0
> Chk= 21 Scr= 1
>

Could you please tell me possible reasons why gaussian gave such an
error?
Could anyone tell me how to fix this problem?

Any suggestions are appreciated.

Thank you very much in advance for your advice.

Best regards,
Takumi

--

Dr. Takumi Hori

Research & Development Laboratories
Nippon Steel Chemical Co., Lid.
46-80 Nakabaru Sakinohama
Tobata-ku, Kitakyushu, Fukuoka 804-8503
Japan
Tel: +81-93-884-1621
Fax: +81-93-884-1923
E-mail: horitk---nscc.co.jp
thori3jp---mac.com
http://www.nscc.co.jp/english/index.html






Now that's room service! Choose from over 150,000 hotels
in 45,000 destinations on Yahoo! Travel to find your fit. --0-302071769-1172034486=:36446-- From owner-chemistry@ccl.net Wed Feb 21 01:50:00 2007 From: "Kirk Peterson kipeters(0)wsu.edu" To: CCL Subject: CCL: Polarization functions for Stuttgart-Dresden basis set? Message-Id: <-33668-070221012602-14579-3NSFZ6+BCRtBysZ7gxY3hw.@.server.ccl.net> X-Original-From: Kirk Peterson Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Tue, 20 Feb 2007 21:33:10 -0800 Mime-Version: 1.0 (Apple Message framework v752.2) Sent to CCL by: Kirk Peterson [kipeters]_[wsu.edu] Jan Martin has published these a few years back: Martin and Sundermann, J. Chem. Phys. 114, 3408 (2001). regards, Kirk Peterson On Feb 20, 2007, at 4:46 PM, Richard A Huhn huhnra#mit.edu wrote: > > Sent to CCL by: "Richard A Huhn" [huhnra _ mit.edu] > Hello, > > Is anyone aware of publications giving polarization functions for > the Stuttgart-Dresden basis set for palladium? Thank you very much > for your help, > > Rich Huhn > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > From owner-chemistry@ccl.net Wed Feb 21 04:29:00 2007 From: "kevin abbot kevanabbot ~ yahoo.com" To: CCL Subject: CCL: query regarding Autodock Message-Id: <-33669-070220112504-9217-IyQ5G8YICWJHSAT//cVxTw[*]server.ccl.net> X-Original-From: kevin abbot Content-Type: multipart/alternative; boundary="0-1707772565-1171985085=:9283" Date: Tue, 20 Feb 2007 07:24:45 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: kevin abbot [kevanabbot-$-yahoo.com] --0-1707772565-1171985085=:9283 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Try this command:=0Aautogrid3 -p file.gpf -l file.glg &=0AIn windows some p= roblems usually occur for AutoDock respect to Linux version.=0ARegards=0A= =0A=0A----- Original Message ----=0AFrom: kalyan chaitanya pulipaka kalyanp= ulipaka|gmail.com =0ATo: "Abbot, Kevin " <= kevanabbot[#]yahoo.com>=0ASent: Friday, February 16, 2007 2:35:24 PM=0ASubjec= t: CCL: query regarding Autodock=0A=0A=0ASent to CCL by: "kalyan chaitanya = pulipaka" [kalyanpulipaka^^^gmail.com]=0Adear all,=0A=0Aiam working on auto= dock windows version...i have also installed cygwin =0Aiam able to =0A-prep= are the PDB file=0A-prepare the Macromolecule=0A-prepare the Ligand=0A-prep= are the gpf file=0Aand i have put all the above prepared files in same fold= er where the Autogrid3 executable is located and when iam launching the com= mand of autogrid3=0A=0A1. thru GUI=0A2. command line of cygwin (autogrid3 -= p abc.gpf -i abc.glg &)=0A=0Ain the first case iam not getting the output f= ile (no maps or glg file)=0A"it says autogrid3 is not recognised as an exte= rnal or internal command" and some times nothing happens like no out put fi= le no error nothing.=0A=0Ain the second case it says "-p , command not foun= d"=0A=0Aplease help me in this regard..=0A=0A=0AThank you in advance=0A=0Ak= alyan.P=0A=0A=0A=0A-=3D This is automatically added to each message by the = mailing script =3D-=0ATo recover the email address of the author of the mes= sage, please change=0Athe strange characters on the top line to the [#] sign.= You can also=0A=0A=0A==0A http://www.ccl.net= /cgi-bin/ccl/send_ccl_message=0A=0AE-mail to administrators: CHEMISTRY-REQU= EST[#]ccl.net or use=0A= =0A=0A=0A http://www.ccl.net/chemistry/sub_unsu= b.shtml=0A=0A=0A=0AJo= b: http://www.ccl.net/jobs =0AConferences: http://server.ccl.net/chemistry/= announcements/conferences/=0A=0ASearch Messages: http://www.ccl.net/htdig = (login: ccl, Password: search)=0A=0AIf your mail bounces from CCL with 5.7.= 1 error, check:=0A=0A=0ARTFI: http://w= ww.ccl.net/chemistry/aboutccl/instructions/=0A=0A-+-+-+-+-+-+-+-+-+-+-+-+-+= -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+=0A=0A=0A =0A________________= ____________________________________________________________________=0AIt's= here! Your new message! =0AGet new email alerts with the free Yahoo! Tool= bar.=0Ahttp://tools.search.yahoo.com/toolbar/features/mail/ --0-1707772565-1171985085=:9283 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Try this command:
=0A
autogrid3 -p = file.gpf -l file.glg &
=0A
In windows some problems usual= ly occur for AutoDock respect to Linux version.
=0A
Regards
=0A
----- Original Message ----
From: kalyan chaita= nya pulipaka kalyanpulipaka|gmail.com <owner-chemistry[#]ccl.net>
To= : "Abbot, Kevin " <kevanabbot[#]yahoo.com>
Sent: Friday, Feb= ruary 16, 2007 2:35:24 PM
Subject: CCL: query regarding Autodock

= =0A
Sent to CCL by: "kalyan chaitanya pulipaka" [kalyanpulipaka^^^gmail= .com]
dear all,

iam working on autodock windows version...i have = also installed cygwin
iam able to
-prepare the PDB file
-prepare= the Macromolecule
-prepare the Ligand
-prepare the gpf file
and i= have put all the above prepared files in same folder where the Autogrid3 e= xecutable is located and when iam launching the command of autogrid3
1. thru GUI
2. command line of cygwin (autogrid3 -p abc.gpf -i abc.glg = &)

in the first case iam not getting the output file (no maps or= glg file)
"it says autogrid3 is not recognised as an external or intern= al command" and some times nothing happens like no out put file no error no= thing.

in the second case it says "-p , command not found"

pl= ease help me in this regard..


Thank you in advance

kalyan= .P



-=3D This is automatically added to each message by the m= ailing script =3D-
To recover the email address of the author of the message, please = change
the strange characters on the top line to the [#] sign. You can als= o
E-mail to= subscribers: CHEMISTRY[#]ccl.net or use:
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If your mail bounces from CCL with 5.7.1 error, ch= eck:
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-+= -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
=0A


=0A=0A
Have a burning q= uestion? Go to Yahoo! Answers and get answers from real people who know. --0-1707772565-1171985085=:9283-- From owner-chemistry@ccl.net Wed Feb 21 08:41:00 2007 From: "Abrash, Samuel sabrash++richmond.edu" To: CCL Subject: CCL:G: G03-Excessive mixing of frozen core and valence orbitals Message-Id: <-33670-070221061427-20516-z0lVAhkLMUy769J+MWtl3g^_^server.ccl.net> X-Original-From: "Abrash, Samuel" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 20 Feb 2007 10:55:03 -0500 MIME-Version: 1.0 Sent to CCL by: "Abrash, Samuel" [sabrash]~[richmond.edu] Hi Ding, You'd said earlier that when you use MP2=full the job works but the Mulliken distributions don't make sense. Its well known that the Mulliken distributions tend to fail when diffuse functions are included in the basis set. Best, Sam -----Original Message----- > From: owner-chemistry*o*ccl.net [mailto:owner-chemistry*o*ccl.net] Sent: Tuesday, February 20, 2007 2:33 AM To: Abrash, Samuel Subject: CCL:G: G03-Excessive mixing of frozen core and valence orbitals Sent to CCL by: Xunlei Ding [dingxunlei[-]gmail.com] Dear David, Thank you very much for your clear explain and suggestions. If this work is done with 6-311++G**, the error is the same: " Largest valence mixing into a core orbital is 9.94D-01 Excessive mixing of frozen core and valence orbitals." And it succeeds with mp2=full. Best regards! Ding Shobe, David David.Shobe---sud-chemie.com wrote: >Sent to CCL by: "Shobe, David" [David.Shobe=sud-chemie.com] >Because you are using ghost atoms, there are empty core orbitals. The HF routine does not distinguish core orbitals from valence orbitals (at least I think this is true), but the MP2 defaults to MP2=FC (frozen core) which of coures does make the distinction. Note that 9.92D-01 = 0.992 = almost full occupancy! > >Perhaps using mp2=full would help, but then you'd have to redo any other mp2 calculations (you have to be consistent: either mp2=full everywhere or mp2=fc everywhere). > >A larger basis set like 6-311+G* or aug-cc-pVTZ is likely to improve matters. With more valence orbitals to choose from, there is less need to use the core orbital. The 6-31G* basis set is too small for accurate calculations of hydrogen bonding energies anyway, if that's what you're after. Again, you'd have to redo any calculations you've already performed using the smaller basis set. > >Regards, >--David Shobe > Süd-Chemie, Inc. > >Attention to detial is essentail. > > >-----Original Message----- > > >>From: owner-chemistry=-=ccl.net [mailto:owner-chemistry=-=ccl.net] >> >> >Sent: Sunday, February 18, 2007 8:39 PM >To: Shobe, David >Subject: CCL:G: G03-Excessive mixing of frozen core and valence orbitals > > >Sent to CCL by: Ding Xunlei [dingxunlei^-^gmail.com] Dear All, > >I did a calculation using mp2 and I find an error below. >Could you give me some suggestion? Thank you! > >This input file: >------------------------------------------------------------ >#mp2/6-31G* > >test > >0 1 > H 0.000000 -0.917747 0.000000 > F 0.000000 0.000000 0.000000 > H 0.000000 1.956639 0.000000 > F 0.000000 2.875828 0.000000 > H 0.000000 -0.917747 -2.250000 > F 0.000000 0.000000 -2.250000 > H-bq 0.000000 1.956639 -2.250000 > F-bq 0.000000 2.875828 -2.250000 > >------------------------------------------------------------ > >The output file: >------------------------------------------------------------------- > SCF Done: E(RHF) = -199.305447100 A.U. after 21 cycles > Convg = 0.2272D-08 -V/T = 1.9654 > S**2 = 0.0000 > ExpMin= 1.61D-01 ExpMax= 7.00D+03 ExpMxC= 1.05D+03 IAcc=1 IRadAn= > 1 AccDes= 1.00D-06 > HarFok: IExCor= 205 AccDes= 1.00D-06 IRadAn= 1 IDoV=1 > ScaDFX= 1.000000 1.000000 1.000000 1.000000 Largest valence mixing into a core orbital is 9.92D-01 Excessive mixing of frozen core and valence orbitals. > Error termination via Lnk1e in /gaussian/03d02-xlf10/g03/l801.exe at Sat Feb 17 16:37:03 2007. > > >Yours sincerely, >Ding Xunlei >2007-02-19 >______________________________________________http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. >Thank you.http://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 21 09:16:00 2007 From: "biplob mondal mondal_biplob123,yahoo.co.in" To: CCL Subject: CCL: mems design prob. Message-Id: <-33671-070221013508-15494-ZWRW2t5blh62dMU1PTqiKw(_)server.ccl.net> X-Original-From: biplob mondal Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1552333729-1172036095=:12605" Date: Wed, 21 Feb 2007 05:34:55 +0000 (GMT) MIME-Version: 1.0 Sent to CCL by: biplob mondal [mondal_biplob123^_^yahoo.co.in] --0-1552333729-1172036095=:12605 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit sir i am working on MEMS design in jadavpur university. i want to the youngs modulas,thermal expansion coeficient and poissons ratio of air. if possible please provide me these datas. looking for ur help. with regards bilpob mondal kadavpur university kolkata,India. --------------------------------- Here’s a new way to find what you're looking for - Yahoo! Answers --0-1552333729-1172036095=:12605 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
sir i am working on MEMS design in jadavpur university. i want to the youngs modulas,thermal expansion coeficient and poissons ratio of air. if possible please provide me these datas.
 
looking for ur help.
 
with regards
bilpob mondal
kadavpur university
kolkata,India.

Here’s a new way to find what you're looking for - Yahoo! Answers --0-1552333729-1172036095=:12605-- From owner-chemistry@ccl.net Wed Feb 21 12:07:00 2007 From: "Carsten Detering detering###biosolveit.de" To: CCL Subject: CCL: FlexX Release 2.1 out now! Message-Id: <-33672-070221120530-27088-ZDaXArFlIDjoaK3DbWvrNw^^server.ccl.net> X-Original-From: "Carsten Detering" Date: Wed, 21 Feb 2007 12:05:27 -0500 Sent to CCL by: "Carsten Detering" [detering _ biosolveit.de] Dear CClers, BioSolveIT is proud to announce the latest Release of the premier docking software FlexX. The package comprises: - A new module FlexX-Screen, which docks a ligand in less than 1 second - Customizable filters including SMARTS (Lipinski, Tox, etc.) - large file support (>2 GB files permissible) - combinatorial de novo docking with pharmacophore constraints - MOE-compatibility - there were no bugs but we fixed them anyway Check out the latest Release of the premier docking engine: http://www.biosolveit.de/flexx BioSolveIT -your developers of FlexX BioSolveIT GmbH - www.biosolveit.de Geschftsfhrer (CEO) Dr. Christian Lemmen Amtsgericht Siegburg HRB 6261 From owner-chemistry@ccl.net Wed Feb 21 13:26:00 2007 From: "Serena Povia sp422-$-cam.ac.uk" To: CCL Subject: CCL: XTL Cerius2 conversion in pdb/xyz/anything else Message-Id: <-33673-070220145406-19860-i0W/ixatjXjgw7zchvKdRA^^^server.ccl.net> X-Original-From: Serena Povia Content-Type: text/plain; format=flowed; charset=ISO-8859-1 Date: 20 Feb 2007 19:21:08 +0000 Mime-Version: 1.0 Sent to CCL by: Serena Povia [sp422===cam.ac.uk] Hello! I was wondering if there is any automatic script/program to convert the XTL cerius format to anything more widely readable (xyz/pdb or anything readable by openbabel). OpenBabel itself doesn't support it, I googled for long time without finding a solution and I don't think that I have enough group theory to attept a script... thank you in advance! Serena -- _ _ _ (o_ Serena Povia (o- (o- //\ Churchill College, Storey's Way (/)_ (\)_ V_/_ CB3 0DS, Cambridge, U.K. -> Is your job running? You'd better go catch it! -> Anyone can make an omelet with eggs. The trick is to make one with none. From owner-chemistry@ccl.net Wed Feb 21 14:59:00 2007 From: "Shobe, David David.Shobe*_*sud-chemie.com" To: CCL Subject: CCL:G: G03-Excessive mixing of frozen core and valence orbitals Message-Id: <-33674-070221143708-23216-VHmze8aBiSsdZ5Ikq6lgrg^server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 21 Feb 2007 20:36:08 +0100 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [David.Shobe|-|sud-chemie.com] Ding, The Mulliken charges you see on H #7 and F #8 are related to the error message you got earlier. It just means that the basis functions on H #7 and F #8 are being occupied in the calculation. What bothers me is the charge of > +7 on F #4. This means that the valence orbitals on F #4 are NOT being used in the wave function!!! You might want to look at the electron density (if you have a suitable visuialization program) to see whether that is strange also. Do you get similar Mulliken charges in a HF calculation? What about other types of charges (NBO, CHELPG, etc.)? Regards, --David Shobe -----Original Message----- > From: owner-chemistry*ccl.net [mailto:owner-chemistry*ccl.net] Sent: Tuesday, February 20, 2007 2:59 AM To: Shobe, David Subject: CCL:G: G03-Excessive mixing of frozen core and valence orbitals Sent to CCL by: Xunlei Ding [dingxunlei:gmail.com] Dear David, Thank you very much for your clear explain and suggestions. If this work is done with mp2(fc)/6-311++G**, the error is the same: " Largest valence mixing into a core orbital is 9.94D-01 Excessive mixing of frozen core and valence orbitals." And it finishes successfully with mp2=full, but the energy is very strange, and also the mulliken charge: Mulliken atomic charges: 1 1 H -1.463786 2 F -0.398420 3 H -0.625697 4 F 7.487903 5 H -1.463786 6 F -0.398420 7 H -1.625697 8 F -1.512097 Also mp2(full)/6-311++G** gives strange energy and mulliken charge. If the work is done with counterpoise=2 or massage, as suggested by Douglas Fox, everything seems ok (both basis sets, and both mp2-full and mp2-fc). So maybe it is a problem of -bq. Best regards! Ding Shobe, David David.Shobe---sud-chemie.com wrote: >Sent to CCL by: "Shobe, David" [David.Shobe=sud-chemie.com] Because you >are using ghost atoms, there are empty core orbitals. The HF routine does not distinguish core orbitals from valence orbitals (at least I think this is true), but the MP2 defaults to MP2=FC (frozen core) which of coures does make the distinction. Note that 9.92D-01 = 0.992 = almost full occupancy! > >Perhaps using mp2=full would help, but then you'd have to redo any other mp2 calculations (you have to be consistent: either mp2=full everywhere or mp2=fc everywhere). > >A larger basis set like 6-311+G* or aug-cc-pVTZ is likely to improve matters. With more valence orbitals to choose from, there is less need to use the core orbital. The 6-31G* basis set is too small for accurate calculations of hydrogen bonding energies anyway, if that's what you're after. Again, you'd have to redo any calculations you've already performed using the smaller basis set. > >Regards, >--David Shobe > Süd-Chemie, Inc. > >Attention to detial is essentail. > > >-----Original Message----- > > >>From: owner-chemistry=-=ccl.net [mailto:owner-chemistry=-=ccl.net] >> >> >Sent: Sunday, February 18, 2007 8:39 PM >To: Shobe, David >Subject: CCL:G: G03-Excessive mixing of frozen core and valence >orbitals > > >Sent to CCL by: Ding Xunlei [dingxunlei^-^gmail.com] Dear All, > >I did a calculation using mp2 and I find an error below. >Could you give me some suggestion? Thank you! > >This input file: >------------------------------------------------------------ >#mp2/6-31G* > >test > >0 1 > H 0.000000 -0.917747 0.000000 > F 0.000000 0.000000 0.000000 > H 0.000000 1.956639 0.000000 > F 0.000000 2.875828 0.000000 > H 0.000000 -0.917747 -2.250000 > F 0.000000 0.000000 -2.250000 > H-bq 0.000000 1.956639 -2.250000 > F-bq 0.000000 2.875828 -2.250000 > >------------------------------------------------------------ > >The output file: >------------------------------------------------------------------- > SCF Done: E(RHF) = -199.305447100 A.U. after 21 cycles > Convg = 0.2272D-08 -V/T = 1.9654 > S**2 = 0.0000 > ExpMin= 1.61D-01 ExpMax= 7.00D+03 ExpMxC= 1.05D+03 IAcc=1 IRadAn= > 1 AccDes= 1.00D-06 > HarFok: IExCor= 205 AccDes= 1.00D-06 IRadAn= 1 IDoV=1 > ScaDFX= 1.000000 1.000000 1.000000 1.000000 Largest valence mixing into a core orbital is 9.92D-01 Excessive mixing of frozen core and valence orbitals. > Error termination via Lnk1e in /gaussian/03d02-xlf10/g03/l801.exe at Sat Feb 17 16:37:03 2007. > > >Yours sincerely, >Ding Xunlei >2007-02-19 >______________________________________________http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. >Thank you.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. Thank you.