From owner-chemistry@ccl.net Mon Jan 28 05:44:01 2008 From: "Igor Avilov avilovi+/-averell.umh.ac.be" To: CCL Subject: CCL:G: G03 Split Basis Set Problems Message-Id: <-36122-080128053541-634-+TjqmewJBQNzeb9ynCiOgQ(~)server.ccl.net> X-Original-From: "Igor Avilov" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="US-ASCII" Date: Mon, 28 Jan 2008 11:03:04 +0100 MIME-Version: 1.0 Sent to CCL by: "Igor Avilov" [avilovi .. averell.umh.ac.be] Dear Kayla, You forgot to include the effective-core potential (pseudopotential) LANL2DZ into the description of the basis. The correct input should be like that: C H F 0 6-311++G** **** Sb 0 LanL2DZ **** Sb 0 LanL2DZ **** Note the empty line between the description of the basis and the pseudopotential. I have a slight concern about the basis you decided to use for lighter elements (6-311++G**), as you basis could be unbalanced as a whole. LANL2DZ does not have neither polarization nor diffuse functions, at least in its default version. Best regards, Igor. -----Original Message----- > From: owner-chemistry*_*ccl.net [mailto:owner-chemistry*_*ccl.net]=20 Sent: samedi 26 janvier 2008 18:06 To: Igor Avilov Subject: CCL:G: G03 Split Basis Set Problems Sent to CCL by: "Kayla M Keller" [k.keller/a\sussex.ac.uk] Hello all,=20 I am relatively new to the field and have recently encountered a problem. =20 I am trying to run a G03 calculation for SbF5 + FCH3 with a split basis (an ECP such as LanL2DZ for Sb and some other basis for the rest of the atoms) using the Gen keyword. However, I keep getting the following warning message:=20 Warning! Sb atom 1 has 51 valence electrons but only 8 basis functions. This is less than a minimal basis set! It also tells me that I have 57 alpha electrons and 57 beta electrons - this is equal to the total number of electrons in the system including the core on Sb that should be frozen. =20 Other things I have tried include but are not limited to: Using the GenECP keyword - the calculation would not run at all. =20 Copying in the basis functions from the http://gnode2.pnl.gov/bse/portal website - this gave a warning that Sb had 51 electrons and 16 basis functions. Has anyone else encountered this problem and found a solution? Here is part of one of my input files:=20 # HF/Gen Opt gfoldprint pop=3Dfull=20 #P GFINPUT IOP(6/7=3D3) =20 =20 Sb-LanL2DZ C_H_F-6-311++G** =20 0 1 Sb 0.371710 -0.011680 0.000000 F 0.530565 1.292165 -1.313374 F -0.250587 -1.205474 1.295313 F 2.130857 -0.574241 0.000002 F 0.530556 1.292153 1.313388 F -0.250580 -1.205462 -1.295327 F -1.654530 0.536415 -0.000002 C -3.066888 -0.039248 0.000000 H -3.675956 0.846378 -0.000010 H -3.103222 -0.617626 -0.906592 H -3.103226 -0.617609 0.906602 =20 C H F 0 6-311++G** **** Sb 0 LanL2DZ **** Thanks in advance, Kayla=20 -- Kayla M. Keller Computational Inorganic Chemistry Turner Group Department of Chemistry University of Sussex Falmer Brighton BN1 9QJ UK k.keller]=3D[sussex.ac.uk -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20http://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Mon Jan 28 07:57:00 2008 From: "akef afaneh akef_afnh_._yahoo.com" To: CCL Subject: CCL:G: G03 Split Basis Set Problems Message-Id: <-36123-080128075414-15988-943p0lG8lT2Wmd2K5i+QEA^server.ccl.net> X-Original-From: akef afaneh Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1430606312-1201521211=:97044" Date: Mon, 28 Jan 2008 03:53:31 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: akef afaneh [akef_afnh{}yahoo.com] --0-1430606312-1201521211=:97044 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi; I think you should use # ****/Gen Pseudo=Read keywords in addition to C H F 0 6-311++G** **** Sb 0 LanL2DZ **** Sb 0 ECP for Sb atom LanL2DZ Use the ECP in this basis set After the molecule specification. You can see the following site: C:\G03W\help\k_pseudo.htm "Igor Avilov avilovi+/-averell.umh.ac.be" wrote: Sent to CCL by: "Igor Avilov" [avilovi .. averell.umh.ac.be] Dear Kayla, You forgot to include the effective-core potential (pseudopotential) LANL2DZ into the description of the basis. The correct input should be like that: C H F 0 6-311++G** **** Sb 0 LanL2DZ **** Sb 0 LanL2DZ **** Note the empty line between the description of the basis and the pseudopotential. I have a slight concern about the basis you decided to use for lighter elements (6-311++G**), as you basis could be unbalanced as a whole. LANL2DZ does not have neither polarization nor diffuse functions, at least in its default version. Best regards, Igor. -----Original Message----- > From: owner-chemistry%a%ccl.net [mailto:owner-chemistry%a%ccl.net] Sent: samedi 26 janvier 2008 18:06 To: Igor Avilov Subject: CCL:G: G03 Split Basis Set Problems Sent to CCL by: "Kayla M Keller" [k.keller/a\sussex.ac.uk] Hello all, I am relatively new to the field and have recently encountered a problem. I am trying to run a G03 calculation for SbF5 + FCH3 with a split basis (an ECP such as LanL2DZ for Sb and some other basis for the rest of the atoms) using the Gen keyword. However, I keep getting the following warning message: Warning! Sb atom 1 has 51 valence electrons but only 8 basis functions. This is less than a minimal basis set! It also tells me that I have 57 alpha electrons and 57 beta electrons - this is equal to the total number of electrons in the system including the core on Sb that should be frozen. Other things I have tried include but are not limited to: Using the GenECP keyword - the calculation would not run at all. Copying in the basis functions from the http://gnode2.pnl.gov/bse/portal website - this gave a warning that Sb had 51 electrons and 16 basis functions. Has anyone else encountered this problem and found a solution? Here is part of one of my input files: # HF/Gen Opt gfoldprint pop=full #P GFINPUT IOP(6/7=3) Sb-LanL2DZ C_H_F-6-311++G** 0 1 Sb 0.371710 -0.011680 0.000000 F 0.530565 1.292165 -1.313374 F -0.250587 -1.205474 1.295313 F 2.130857 -0.574241 0.000002 F 0.530556 1.292153 1.313388 F -0.250580 -1.205462 -1.295327 F -1.654530 0.536415 -0.000002 C -3.066888 -0.039248 0.000000 H -3.675956 0.846378 -0.000010 H -3.103222 -0.617626 -0.906592 H -3.103226 -0.617609 0.906602 C H F 0 6-311++G** **** Sb 0 LanL2DZ **** Thanks in advance, Kayla -- Kayla M. Keller Computational Inorganic Chemistry Turner Group Department of Chemistry University of Sussex Falmer Brighton BN1 9QJ UK k.keller]=[sussex.ac.ukhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/spammers.txthttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--------------------------------- Never miss a thing. Make Yahoo your homepage. --0-1430606312-1201521211=:97044 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Hi;
I think you should use # ****/Gen Pseudo=Read keywords in addition to 
C H F 0
6-311++G**
****
Sb 0
LanL2DZ
****
 
Sb 0                                         ECP for Sb atom
LanL2DZ                                 Use the ECP in this basis set
 
After the molecule specification. You can see the following
 site:
C:\G03W\help\k_pseudo.htm


"Igor Avilov avilovi+/-averell.umh.ac.be" <owner-chemistry__ccl.net> wrote:

Sent to CCL by: "Igor Avilov" [avilovi .. averell.umh.ac.be]
Dear Kayla,

You forgot to include the effective-core potential (pseudopotential)
LANL2DZ into the description of the basis. The correct input should be
like that:

C H F 0
6-311++G**
****
Sb 0
LanL2DZ
****

Sb 0
LanL2DZ
****

Note the empty line between the description of the basis and the
pseudopotential.

I have a slight concern about the basis you decided to use for lighter
elements (6-311++G**), as you basis could be unbalanced as a whole.
LANL2DZ does not have neither polarization nor diffuse functions, at
least in its default version.

Best regards,
Igor.


-----Original Message-----
> From: owner-chemistry%a%ccl.net [mailto:owner-chemistry%a%ccl.net]
Sent: samedi 26 janvier 2008 18:06
To: Igor Avilov
Subject: CCL:G: G03 Split Basis Set Problems


Sent to CCL by: "Kayla M Keller" [k.keller/a\sussex.ac.uk] Hello all,

I am relatively new to the field and have recently encountered a
problem.

I am trying to run a G03 calculation for SbF5 + FCH3 with a split basis
(an ECP such as LanL2DZ for Sb and some other basis for the rest of the
atoms) using the Gen keyword. However, I keep getting the following
warning message:
Warning! Sb atom 1 has 51 valence electrons but only 8 basis
functions.
This is less than a minimal basis set!

It also tells me that I have 57 alpha electrons and 57 beta electrons -
this is equal to the total number of electrons in the system including
the core on Sb that should be frozen.

Other things I have tried include but are not limited to:
Using the GenECP keyword - the calculation would not run at all.
Copying in the basis functions from the http://gnode2.pnl.gov/bse/portal
website - this gave a warning that Sb had 51 electrons and 16 basis
functions.

Has anyone else encountered this problem and found a solution?

Here is part of one of my input files:
# HF/Gen Opt gfoldprint pop=full
#P GFINPUT IOP(6/7=3)


Sb-LanL2DZ C_H_F-6-311++G**


0 1
Sb 0.371710 -0.011680 0.000000
F 0.530565 1.292165 -1.313374
F -0.250587 -1.205474 1.295313
F 2.130857 -0.574241 0.000002
F 0.530556 1.292153 1.313388
F -0.250580 -1.205462 -1.295327
F -1.654530 0.536415 -0.000002
C -3.066888 -0.039248 0.000000
H -3.675956 0.846378 -0.000010
H -3.103222 -0.617626 -0.906592
H -3.103226 -0.617609 0.906602

C H F 0
6-311++G**
****
Sb 0
LanL2DZ
****

Thanks in advance,
Kayla

--
Kayla M. Keller

Computational Inorganic Chemistry

Turner Group

Department of Chemistry
University of Sussex
Falmer
Brighton
BN1 9QJ
UK

k.keller]=[sussex.ac.uk



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Never miss a thing. Make Yahoo your homepage. --0-1430606312-1201521211=:97044-- From owner-chemistry@ccl.net Mon Jan 28 08:56:01 2008 From: "abdeladim guermoune lguermoune*_*hotmail.com" To: CCL Subject: CCL:G: problem with aim calculation. Message-Id: <-36124-080128085236-9767-xS4O7mpTks+17w57CgAFfg=server.ccl.net> X-Original-From: "abdeladim guermoune" Date: Mon, 28 Jan 2008 08:52:33 -0500 Sent to CCL by: "abdeladim guermoune" [lguermoune,hotmail.com] Dear members, I try to run a calculation in G03 with aim instructions To find a critical points for geometries including Iron and bridged hydrogen between borons atoms (tree centers two electrons) But I get de following message in the end of the output file: THE MOLECULAR GRAPH IS DISCONNECTED ... ABORTING! Error termination via Lnk1e in /users/g03/l609.exe at Sun Jan 27 23:33:36 2008. I used as keywords in the input file: #p B3P86 6-311++G(3df,2p) aim=all density=current scf=(tight,save) output=wfn scfcyc=250 guess=huckel Can any one have suggestions to result this problem? (sorry for my English, its the third foreigner language for me) Yours, ----------------------------------- GUERMOUNE Abdeladim. University Cadi Ayyad Morocco. From owner-chemistry@ccl.net Mon Jan 28 09:31:00 2008 From: "Dr. M. Qaiser Fatmi qaiser_fatmi__yahoo.com" To: CCL Subject: CCL:G: G03 Split Basis Set Problems Message-Id: <-36125-080128021149-16333-om6U+3TMoL0jyI7yPy4jfg^-^server.ccl.net> X-Original-From: "Dr. M. Qaiser Fatmi" Content-Type: multipart/alternative; boundary="0-569737789-1201500693=:20564" Date: Sun, 27 Jan 2008 22:11:33 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: "Dr. M. Qaiser Fatmi" [qaiser_fatmi(0)yahoo.com] --0-569737789-1201500693=:20564 Content-Type: text/plain; charset=us-ascii Dear Keller, Are you sure that the structure you have drawn is correct.. Dr. M. Qaiser Fatmi PhD (Computational Chemistry, Austria) http://fatmiqaiser.googlepages.com ----- Original Message ---- > From: Kayla M Keller k.keller[]sussex.ac.uk To: "Fatmi, Muhammad Qaiser " Sent: Saturday, January 26, 2008 12:05:38 PM Subject: CCL:G: G03 Split Basis Set Problems Sent to CCL by: "Kayla M Keller" [k.keller/a\sussex.ac.uk] Hello all, I am relatively new to the field and have recently encountered a problem. I am trying to run a G03 calculation for SbF5 + FCH3 with a split basis (an ECP such as LanL2DZ for Sb and some other basis for the rest of the atoms) using the Gen keyword. However, I keep getting the following warning message: Warning! Sb atom 1 has 51 valence electrons but only 8 basis functions. This is less than a minimal basis set! It also tells me that I have 57 alpha electrons and 57 beta electrons - this is equal to the total number of electrons in the system including the core on Sb that should be frozen. Other things I have tried include but are not limited to: Using the GenECP keyword - the calculation would not run at all. Copying in the basis functions from the http://gnode2.pnl.gov/bse/portal website - this gave a warning that Sb had 51 electrons and 16 basis functions. Has anyone else encountered this problem and found a solution? Here is part of one of my input files: # HF/Gen Opt gfoldprint pop=full #P GFINPUT IOP(6/7=3) Sb-LanL2DZ C_H_F-6-311++G** 0 1 Sb 0.371710 -0.011680 0.000000 F 0.530565 1.292165 -1.313374 F -0.250587 -1.205474 1.295313 F 2.130857 -0.574241 0.000002 F 0.530556 1.292153 1.313388 F -0.250580 -1.205462 -1.295327 F -1.654530 0.536415 -0.000002 C -3.066888 -0.039248 0.000000 H -3.675956 0.846378 -0.000010 H -3.103222 -0.617626 -0.906592 H -3.103226 -0.617609 0.906602 C H F 0 6-311++G** **** Sb 0 LanL2DZ **** Thanks in advance, Kayla -- Kayla M. Keller Computational Inorganic Chemistry Turner Group Department of Chemistry University of Sussex Falmer Brighton BN1 9QJ UK k.keller]=[sussex.ac.ukhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt____________________________________________________________________________________ Never miss a thing. Make Yahoo your home page. http://www.yahoo.com/r/hs --0-569737789-1201500693=:20564 Content-Type: text/html; charset=us-ascii
Dear Keller,
Are you sure that the structure you have drawn is correct..
 
Dr. M. Qaiser Fatmi
PhD (Computational Chemistry, Austria)
http://fatmiqaiser.googlepages.com


----- Original Message ----
From: Kayla M Keller k.keller[]sussex.ac.uk <owner-chemistry]|[ccl.net>
To: "Fatmi, Muhammad Qaiser " <qaiser_fatmi]|[yahoo.com>
Sent: Saturday, January 26, 2008 12:05:38 PM
Subject: CCL:G: G03 Split Basis Set Problems


Sent to CCL by: "Kayla  M  Keller" [k.keller/a\sussex.ac.uk]
Hello all,

I am relatively new to the field and have recently encountered a problem. 

I am trying to run a G03 calculation for SbF5 + FCH3 with a split basis (an ECP such as LanL2DZ for Sb and some other basis for the rest of the atoms) using the Gen keyword.  However, I keep getting the following warning message:
Warning!  Sb atom    1 has 51 valence electrons but only  8 basis functions.
This is less than a minimal basis set!

It also tells me that I have  57 alpha electrons and 57 beta electrons - this is equal to the total number of electrons in the system including the core on Sb that should be frozen. 

Other things I have tried include but are not limited to:
Using the GenECP keyword - the calculation would not run at all. 
Copying in the basis functions from the http://gnode2.pnl.gov/bse/portal website - this gave a warning that Sb had 51 electrons and 16 basis functions.

Has anyone else encountered this problem and found a solution?

Here is part of one of my input files:
# HF/Gen Opt gfoldprint pop=full
#P GFINPUT IOP(6/7=3)   
                                                                             
Sb-LanL2DZ C_H_F-6-311++G**
                                                                             
0 1
Sb      0.371710  -0.011680    0.000000
F        0.530565    1.292165  -1.313374
F      -0.250587  -1.205474    1.295313
F        2.130857  -0.574241    0.000002
F        0.530556    1.292153    1.313388
F      -0.250580  -1.205462  -1.295327
F      -1.654530    0.536415  -0.000002
C      -3.066888  -0.039248    0.000000
H      -3.675956    0.846378  -0.000010
H      -3.103222  -0.617626  -0.906592
H      -3.103226  -0.617609    0.906602
                                                                   
C H F 0
6-311++G**
****
Sb 0
LanL2DZ
****

Thanks in advance,
Kayla

--
Kayla M. Keller

Computational Inorganic Chemistry

Turner Group

Department of Chemistry
University of Sussex
Falmer
Brighton
BN1 9QJ
UK

k.keller]=[sussex.ac.uk



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Diaconu" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 28 Jan 2008 01:45:24 -0700 MIME-Version: 1.0 Sent to CCL by: "Cristian V. Diaconu" [cvdiaconu,lanl.gov] Your probably forgot to put the ECP for Sb after the basis or did not leave a blank line, so gaussian thinks that Sb has all its electrons, while your basis set has functions only for the valence space. Here is a sample input file with ECP: #p b3lyp/genecp pt-porphine 0 1 Pt 0.00000000 0.00000000 0.00000000 N 0.00000000 2.00623054 -0.00000000 .... H -3.18868075 3.18868075 -0.00000000 Pt 0 S 1 1.0 2.5470 -1.4739175 ... D 1 1.0 0.1370 1.0000000 **** C H N 0 6-31g* **** Pt 0 lanl2 Don't forget the blank line after ecp definition! Good look! Chris Kayla M Keller k.keller[]sussex.ac.uk wrote: > Sent to CCL by: "Kayla M Keller" [k.keller/a\sussex.ac.uk] > Hello all, > > I am relatively new to the field and have recently encountered a problem. > > I am trying to run a G03 calculation for SbF5 + FCH3 with a split basis (an ECP such as LanL2DZ for Sb and some other basis for the rest of the atoms) using the Gen keyword. However, I keep getting the following warning message: > Warning! Sb atom 1 has 51 valence electrons but only 8 basis functions. > This is less than a minimal basis set! > > It also tells me that I have 57 alpha electrons and 57 beta electrons - this is equal to the total number of electrons in the system including the core on Sb that should be frozen. > > Other things I have tried include but are not limited to: > Using the GenECP keyword - the calculation would not run at all. > Copying in the basis functions from the http://gnode2.pnl.gov/bse/portal website - this gave a warning that Sb had 51 electrons and 16 basis functions. > > Has anyone else encountered this problem and found a solution? > > Here is part of one of my input files: > # HF/Gen Opt gfoldprint pop=full > #P GFINPUT IOP(6/7=3) > > Sb-LanL2DZ C_H_F-6-311++G** > > 0 1 > Sb 0.371710 -0.011680 0.000000 > F 0.530565 1.292165 -1.313374 > F -0.250587 -1.205474 1.295313 > F 2.130857 -0.574241 0.000002 > F 0.530556 1.292153 1.313388 > F -0.250580 -1.205462 -1.295327 > F -1.654530 0.536415 -0.000002 > C -3.066888 -0.039248 0.000000 > H -3.675956 0.846378 -0.000010 > H -3.103222 -0.617626 -0.906592 > H -3.103226 -0.617609 0.906602 > > C H F 0 > 6-311++G** > **** > Sb 0 > LanL2DZ > **** > > Thanks in advance, > Kayla > > -- > Kayla M. Keller > > Computational Inorganic Chemistry > > Turner Group > > Department of Chemistry > University of Sussex > Falmer > Brighton > BN1 9QJ > UK > > k.keller]=[sussex.ac.uk> > > -- Cristian V. Diaconu Postdoctoral Research Associate Los Alamos National Laboratory Theoretical Division Theoretical Chemistry & Molecular Physics Group (T-12) Mail Stop B268 Los Alamos, NM 87545 Phone: 505-665-2635 Fax: 505-665-3909 E-mail: cvdiaconu * lanl.gov From owner-chemistry@ccl.net Mon Jan 28 13:00:00 2008 From: "Rzepa, Henry h.rzepa[a]imperial.ac.uk" To: CCL Subject: CCL:G: problem with aim calculation. Message-Id: <-36128-080128120557-16618-oiVVbgUq5mRy/5YzCcHa4g/./server.ccl.net> X-Original-From: "Rzepa, Henry" Content-Type: text/plain; charset="us-ascii" Date: Mon, 28 Jan 2008 15:44:02 +0000 Mime-Version: 1.0 Sent to CCL by: "Rzepa, Henry" [h.rzepa^imperial.ac.uk] >Sent to CCL by: "abdeladim guermoune" [lguermoune,hotmail.com] >Dear members, >I try to run a calculation in G03 with aim instructions >To find a critical points for geometries including >Iron and bridged hydrogen between borons atoms (tree centers two electrons) >But I get de following message in the end of the output file: > >THE MOLECULAR GRAPH IS DISCONNECTED ... ABORTING! > Error termination via Lnk1e in /users/g03/l609.exe at Sun Jan 27 23:33:36 2008. The G03 implementation is both old and unsupported/undocumented. Old code never seems to die in Gaussian, it just fades away. Even if you get past the above message, more often than not the Poincare-Hopf condition will not be satisfied either! You are better transferring the wfn file to a program such as AIM2000 or Morphy. By the way, if anyone does plan on using output=wfn, you will have to edit the resulting file if you have more than 99 atoms, since the good old Fortran output statement is I2,1X, and hence the 100th atom will catenate. If however, spaces are added to the relevant output (or the Gaussian format statement changed), all is OK. Oh, can any expert on AIM comment on the interesting "artefacts" obtained when one of the elements has a pseudopotential? Various bond critical bonds very close to the nucleus appear. Do they mean anything? -- Henry Rzepa. +44 (020) 7594 5774 (Voice); +44 (0870) 132 3747 (eFax); rzepahs[]mac.com (iChat) http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, SW7 2AZ, UK. (Voracious anti-spam filter in operation for received email. If expected reply not received, please phone/fax). From owner-chemistry@ccl.net Mon Jan 28 13:58:01 2008 From: "Soren Eustis soreneustis|,|gmail.com" To: CCL Subject: CCL:G: G03 Split Basis Set Problems Message-Id: <-36129-080128135140-17862-71ka0UC3iFOIbTJDpLj1Zw]-[server.ccl.net> X-Original-From: "Soren Eustis" Content-language: en-us Content-Type: multipart/alternative; boundary="----=_NextPart_000_001D_01C861A5.4F391BE0" Date: Mon, 28 Jan 2008 11:59:59 -0500 MIME-Version: 1.0 Sent to CCL by: "Soren Eustis" [soreneustis]_[gmail.com] This is a multipart message in MIME format. ------=_NextPart_000_001D_01C861A5.4F391BE0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit This should work using genecp. The errors are because the ECP portion is not being incorporated correctly. I have experienced this before. I would suggest pasting in the entire output from EMSL such as: . C H F 0 6-311++G** **** ! LANL2DZ ECP EMSL Basis Set Exchange Library 1/28/08 8:56 AM ! Elements References ! -------- ---------- ! H - Ne: T. H. Dunning Jr. and P. J. Hay, in Methods of Electronic Structure ! Theory, Vol. 2, H. F. Schaefer III, ed., PLENUM PRESS (1977) ! Na - Hg: P. J. Hay and W. R. Wadt, J. Chem. Phys. 82, 270 (1985). ! P. J. Hay and W. R. Wadt, J. Chem. Phys. 82, 284 (1985). ! P. J. Hay and W. R. Wadt, J. Chem. Phys. 82, 299 (1985). ! PB 0 S 2 1.00 0.5135000 -4.3675036 0.3756000 4.8504656 S 1 1.00 0.0944000 1.0000000 P 2 1.00 0.8748000 -0.1793128 0.1843000 1.0776505 P 1 1.00 0.0598000 1.0000000 **** ! Elements References ! -------- ---------- ! Na - Hg: P. J. Hay and W. R. Wadt, J. Chem. Phys. 82, 270 (1985). ! P. J. Hay and W. R. Wadt, J. Chem. Phys. 82, 284 (1985). ! P. J. Hay and W. R. Wadt, J. Chem. Phys. 82, 299 (1985). ! PB 0 PB-ECP 4 78 g potential 6 0 376.5803786 -0.1789605 1 86.4840014 -54.3972337 2 26.6784276 -199.7061759 2 9.4261986 -79.1223941 2 2.7101719 -24.9869020 2 0.8792031 -4.4397939 s-g potential 6 0 132.4248796 2.8115386 1 47.2376044 65.0367205 2 17.6312727 212.7868545 2 5.4744712 72.1053175 2 1.2634856 33.0140940 2 0.7651447 -5.7708461 p-g potential 6 0 67.8966454 4.8754911 1 24.9898225 63.9148102 2 10.7052939 148.1064358 2 3.2792568 47.3106301 2 0.8452522 21.0306702 2 0.6416245 -7.0930772 d-g potential 6 0 68.8336005 3.2161388 1 24.2815874 55.7386086 2 9.4532762 121.4168351 2 2.4788185 19.3456064 2 2.4789161 15.3675168 2 0.5551738 6.1298724 f-g potential 6 0 128.1021322 4.1353682 1 54.8029154 67.5128446 2 24.5529308 258.7373107 2 8.1144792 113.2478264 2 1.6931290 34.1680201 2 0.7670500 -6.5531956 Note: Gaussian wants a space at the end of the file and one before the ECP parameters. Regards, Soren Eustis > From: owner-chemistry-$-ccl.net [mailto:owner-chemistry-$-ccl.net] Sent: Monday, January 28, 2008 1:12 AM To: Eustis, Soren Subject: CCL:G: G03 Split Basis Set Problems Dear Keller, Are you sure that the structure you have drawn is correct.. _____ Dr. M. Qaiser Fatmi PhD (Computational Chemistry, Austria) http://fatmiqaiser.googlepages.com _____ ----- Original Message ---- > From: Kayla M Keller k.keller[]sussex.ac.uk To: "Fatmi, Muhammad Qaiser " Sent: Saturday, January 26, 2008 12:05:38 PM Subject: CCL:G: G03 Split Basis Set Problems Sent to CCL by: "Kayla M Keller" [k.keller/a\sussex.ac.uk] Hello all, I am relatively new to the field and have recently encountered a problem. I am trying to run a G03 calculation for SbF5 + FCH3 with a split basis (an ECP such as LanL2DZ for Sb and some other basis for the rest of the atoms) using the Gen keyword. However, I keep getting the following warning message: Warning! Sb atom 1 has 51 valence electrons but only 8 basis functions. This is less than a minimal basis set! It also tells me that I have 57 alpha electrons and 57 beta electrons - this is equal to the total number of electrons in the system including the core on Sb that should be frozen. Other things I have tried include but are not limited to: Using the GenECP keyword - the calculation would not run at all. Copying in the basis functions from the http://gnode2.pnl.gov/bse/portal website - this gave a warning that Sb had 51 electrons and 16 basis functions. Has anyone else encountered this problem and found a solution? Here is part of one of my input files: # HF/Gen Opt gfoldprint pop=full #P GFINPUT IOP(6/7=3) Sb-LanL2DZ C_H_F-6-311++G** 0 1 Sb 0.371710 -0.011680 0.000000 F 0.530565 1.292165 -1.313374 F -0.250587 -1.205474 1.295313 F 2.130857 -0.574241 0.000002 F 0.530556 1.292153 1.313388 F -0.250580 -1.205462 -1.295327 F -1.654530 0.536415 -0.000002 C -3.066888 -0.039248 0.000000 H -3.675956 0.846378 -0.000010 H -3.103222 -0.617626 -0.906592 H -3.103226 -0.617609 0.906602 C H F 0 6-311++G** **** Sb 0 LanL2DZ **** Thanks in advance, Kayla -- Kayla M. Keller Computational Inorganic Chemistry Turner Group Department of Chemistry University of Sussex Falmer Brighton BN1 9QJ UK k.keller]=[sussex.ac.uk them fast with Yahoo! Search. ------=_NextPart_000_001D_01C861A5.4F391BE0 Content-Type: text/html; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable

This should work using genecp.  The errors are = because the ECP portion is not being incorporated correctly.  I have = experienced this before. I would suggest pasting in the entire output from EMSL such = as:

 

…

C H F 0
6-311++G**
****

!  LANL2DZ ECP  EMSL  Basis Set = Exchange Library   1/28/08 8:56 AM

! Elements           = ;            =       References

! --------           = ;            =       ----------

! H  - Ne: T. H. Dunning Jr. and P. J. Hay, in Methods of Electronic Structure

!        &nb= sp; Theory, Vol. 2, H. F. Schaefer III, ed., PLENUM PRESS = (1977)

! Na - Hg: P. J. Hay and W. R. Wadt, J. Chem. Phys. = 82, 270 (1985).

!        &nb= sp; P. J. Hay and W. R. Wadt, J. Chem. Phys. 82, 284 = (1985).

!        &nb= sp; P. J. Hay and W. R. Wadt, J. Chem. Phys. 82, 299 = (1985).

!

PB     0

S     2     = 1.00

        &nbs= p;    0.5135000          &nbs= p;  -4.3675036        =

  =            0.37560= 00            = ;  4.8504656        =

S     1     = 1.00

        &nbs= p;    0.0944000          &nbs= p;   1.0000000        =

P     2     = 1.00

        &nbs= p;    0.8748000          &nbs= p;  -0.1793128        =

        &nbs= p;    0.1843000          &nbs= p;   1.0776505        =

P     1     = 1.00

        &nbs= p;    0.0598000          &nbs= p;   1.0000000        =

****

! Elements           = ;            =       References

! --------           = ;            =       ----------

! Na - Hg: P. J. Hay and W. R. Wadt, J. Chem. Phys. = 82, 270 (1985).

!        &nb= sp; P. J. Hay and W. R. Wadt, J. Chem. Phys. 82, 284 = (1985).

!        &nb= sp; P. J. Hay and W. R. Wadt, J. Chem. Phys. 82, 299 = (1985).

!

  

PB     0

PB-ECP   4   = 78

g potential

  6          =

0        &nb= sp;   376.5803786          &n= bsp;  -0.1789605        =

1        &nb= sp;    86.4840014          &nb= sp; -54.3972337        =

2        &nb= sp;    26.6784276           -199.7061759        =

2        &nb= sp;     9.4261986          &nbs= p; -79.1223941        =

2        &nb= sp;     2.7101719          &nbs= p; -24.9869020        =

2        &nb= sp;     0.8792031          &nbs= p;  -4.4397939        =

s-g potential

  6          =

0        &nb= sp;   132.4248796          &n= bsp;   2.8115386        =

1        &nb= sp;    47.2376044          &nb= sp;  65.0367205        =

2        &nb= sp;    17.6312727          &nb= sp; 212.7868545        =

2        &nb= sp;     5.4744712          &nbs= p;  72.1053175   =      

2        &nb= sp;     1.2634856          &nbs= p;  33.0140940        =

2        &nb= sp;     0.7651447          &nbs= p;  -5.7708461        =

p-g potential

  6          =

0        &nb= sp;    67.8966454          &nb= sp;   4.8754911        =

1        &nb= sp;    24.9898225          &nb= sp;  63.9148102       =  

2        &nb= sp;    10.7052939          &nb= sp; 148.1064358        =

2        &nb= sp;     3.2792568          &nbs= p;  47.3106301        =

2        &nb= sp;     0.8452522          &nbs= p;  21.0306702        =

2        &nb= sp;     0.6416245          &nbs= p;  -7.0930772        =

d-g potential

  6          =

0 =             6= 8.8336005          &nbs= p;   3.2161388        =

1        &nb= sp;    24.2815874          &nb= sp;  55.7386086        =

2        &nb= sp;     9.4532762          &nbs= p; 121.4168351        =

2        &nb= sp;     2.4788185          &nbs= p;  19.3456064        =

2        &nb= sp;     2.4789161          =    15.3675168       

2        &nb= sp;     0.5551738          &nbs= p;   6.1298724        =

f-g potential

  6          =

0        &nb= sp;   128.1021322          &n= bsp;   4.1353682        =

1        &nb= sp;    54.8029154          &nb= sp;  67.5128446        =

2        &nb= sp;    24.5529308          &nb= sp; 258.7373107       

2        &nb= sp;     8.1144792          &nbs= p; 113.2478264        =

2        &nb= sp;     1.6931290          &nbs= p;  34.1680201        =

2        &nb= sp;     0.7670500          &nbs= p;  -6.5531956  

 

 

 

 

Note:  Gaussian wants a space at the end of = the file and one before the ECP parameters.

 

Regards,

 

Soren Eustis     =

 

 

 

 

 

From:= = owner-chemistry-$-ccl.net [mailto:owner-chemistry-$-ccl.net]
Sent: Monday, January 28, 2008 1:12 AM
To: Eustis, Soren
Subject: CCL:G: G03 Split Basis Set = Problems

 

Dear Keller,
Are you sure that the structure you have drawn is = correct..

 

Dr. M. Qaiser Fatmi PhD (Computational Chemistry, = Austria)
http://fatmiqaiser.googlepages.c= om

 

----- Original = Message ----
> From: Kayla M Keller k.keller[]sussex.ac.uk = <owner-chemistry-x-ccl.net>
To: "Fatmi, Muhammad Qaiser " = <qaiser_fatmi-x-yahoo.com>
Sent: Saturday, January 26, 2008 12:05:38 PM
Subject: CCL:G: G03 Split Basis Set Problems


Sent to CCL by: "Kayla  M  Keller" [k.keller/a\sussex.ac.uk]
Hello all,

I am relatively new to the field and have recently encountered a = problem. 

I am trying to run a G03 calculation for SbF5 + FCH3 with a split basis = (an ECP such as LanL2DZ for Sb and some other basis for the rest of the atoms) = using the Gen keyword.  However, I keep getting the following warning = message:
Warning!  Sb atom    1 has 51 valence electrons but = only  8 basis functions.
This is less than a minimal basis set!

It also tells me that I have  57 alpha electrons and 57 beta = electrons - this is equal to the total number of electrons in the system including = the core on Sb that should be frozen. 

Other things I have tried include but are not limited to:
Using the GenECP keyword - the calculation would not run at all.  =
Copying in the basis functions from the http://gnode2.pnl.gov/bse/portal website - this gave a warning that Sb had 51 electrons and 16 basis = functions.

Has anyone else encountered this problem and found a solution?

Here is part of one of my input files:
# HF/Gen Opt gfoldprint pop=3Dfull
#P GFINPUT IOP(6/7=3D3)   
                    =                       =                       =              
Sb-LanL2DZ C_H_F-6-311++G**
                    =                       =                       =              
0 1
Sb      0.371710  -0.011680    = 0.000000
F        0.530565    1.292165  = -1.313374
F      -0.250587  -1.205474    = 1.295313
F        2.130857  -0.574241    = 0.000002
F        0.530556    1.292153    1.313388
F      -0.250580  -1.205462  -1.295327
F      -1.654530    0.536415  = -0.000002
C      -3.066888  -0.039248    = 0.000000
H      -3.675956    0.846378  = -0.000010
H      -3.103222  -0.617626  -0.906592
H      -3.103226  -0.617609    = 0.906602
                    =                       =                       =    
C H F 0
6-311++G**
****
Sb 0
LanL2DZ
****

Thanks in advance,
Kayla

--
Kayla M. Keller

Computational Inorganic Chemistry

Turner Group

Department of Chemistry
University of Sussex
Falmer
Brighton
BN1 9QJ
UK

k.keller]=3D[sussex.ac.uk


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------=_NextPart_000_001D_01C861A5.4F391BE0-- From owner-chemistry@ccl.net Mon Jan 28 16:03:00 2008 From: "Alexander Hoepker achoepker:+:gmail.com" To: CCL Subject: CCL:G: memory problem in Gaussian Message-Id: <-36130-080128152228-22024-KIZgy792kc6ArT6qtAI3HQ . server.ccl.net> X-Original-From: "Alexander Hoepker" Content-Type: multipart/alternative; boundary="----=_Part_9173_18204638.1201547918505" Date: Mon, 28 Jan 2008 14:18:38 -0500 MIME-Version: 1.0 Sent to CCL by: "Alexander Hoepker" [achoepker|gmail.com] ------=_Part_9173_18204638.1201547918505 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline I'm running out of memory during one of my transition state calculation in Gaussian 03. Even though the atom size is smaller than others that have worked before, the computer runs out of memory during its initial frequency calculation. I tried to solve this issue in three ways: (1) restrict the three atoms that are described by the imaginary frequency, optimize this and resubmit to an unconstrained TS calculation. (2) solve the memory issue by splitting the file into five chunks (r1-r5) each being slightly less than 2GB (250MW). usr2/GAUSS_SCR is the scratch directory. I'm using a 32 bit computer. %RWF=/usr2/GAUSS_SCR/r1,249MW,/usr2/GAUSS_SCR/r2,249MW,/usr2/ GAUSS_SCR/r3,249MW,/usr2/GAUSS_SCR/r4,249MW,/usr2/GAUSS_SCR/r5 ,249MW Both approaches fail by crashing at the frequency calculation. Does anyone have a suggestion? Thanks is advance ------=_Part_9173_18204638.1201547918505 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline I'm running out of memory during one of my transition state calculation in Gaussian 03. Even though the atom size is smaller than others that have worked before, the computer runs out of memory during its initial frequency calculation. I tried to solve this issue in three ways:

(1) restrict the three atoms that are described by the imaginary frequency, optimize this and resubmit to an unconstrained TS calculation.

(2) solve the memory issue by splitting the file into five chunks (r1-r5) each being slightly less than 2GB (250MW).  usr2/GAUSS_SCR is the scratch directory. I'm using a 32 bit computer.

%RWF=/usr2/GAUSS_SCR/r1,249MW,/usr2/GAUSS_SCR/r2,249MW,/usr2/

GAUSS_SCR/r3,249MW,/usr2/GAUSS_SCR/r4,249MW,/usr2/GAUSS_SCR/r5

,249MW


Both approaches fail by crashing at the frequency calculation. Does anyone have a suggestion?


Thanks is advance

------=_Part_9173_18204638.1201547918505-- From owner-chemistry@ccl.net Mon Jan 28 16:37:01 2008 From: "Geoff Skillman skillman,,eyesopen.com" To: CCL Subject: CCL: LASSO paper and SimBioSys blog Message-Id: <-36131-080128151910-21681-FJWn9HttILgkWwuv9rFtXg_+_server.ccl.net> X-Original-From: Geoff Skillman Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 28 Jan 2008 13:19:08 -0700 MIME-Version: 1.0 Sent to CCL by: Geoff Skillman [skillman=eyesopen.com] Dear Aniko- Perhaps you should apply your new technology to the "Statistical Assessment of the Modeling of Proteins and Ligands" (SAMPL). It is a blinded trial of virtual screening, pose-prediction and affinity prediction based on proprietary data from Abbott Laboratories and Vertex Pharmaceuticals. Several academic groups and software vendors from the virtual screening field are participating. It would be a good opportunity to demonstrate how LASSO compares to other virtual screening methods. You can sign up for the evaluation and get further details at http://sampl.eyesopen.com SAMPL also includes a blinded transfer energy prediction data set. Best Regards, Geoff Skillman Aniko Simon aniko ~~ simbiosys.ca wrote: > Sent to CCL by: "Aniko Simon" [aniko/a\simbiosys.ca] > SimBioSys would like to make two announcements: > > 1) Our publication regarding "LASSO-ligand activity by surface similarity order: a new tool for ligand based virtual screening" has just been published in the Journal of Computer-Aided Molecular Design and is available at this link: http://dx.doi.org/10.1007/s10822-007-9164-5. LASSO is a ligand-based similarity search tool that uses surface properties of known active molecules to build a model for screening large databases for molecules with similar properties. The tool is extremely fast and can screen a database of a million molecules in under 1 minute on a standard single CPU machine. LASSO is independent of the underlying 2D skeleton or the 3D conformation and has the ability to retrieve molecules with very different 2D scaffolds (chemotypes) without the need for a bioactive conformation. > > LASSO is the basis of exciting work presently underway with ChemSpider (www.chemspider.com). We have teamed up to provide the virtual screening results for 40 target families on the full ChemSpider Library, currently containing over 18 million molecules. Using the LASSO similarity search tool, SimBioSys has screened the ChemSpider database against all 40 target families from the Database of Useful Decoys (DUD) dataset. The work is discussed in a little more detail on their blog at http://www.chemspider.com/blog/announcing-the-chemspider-ligand-activity-project-partnering-with-simbiosys.html. We will also cover the developments at http://www.simbiosys.ca/lasso/publications.html > > > 2) The SimBioSys blog is now online: http://www.simbiosys.ca/blog/. The purpose behind this blog has already been discussed in the opening blogpost (http://www.simbiosys.ca/blog/2008/01/09/welcome-hello-world-lets-begin-the-discussion/). We look forward to engaging scientists in active discussions on our blog and keeping everyone updated with our developments, specifically our work to utilize high performance computing for the purpose of accelerated docking (see the White Paper http://www.simbiosys.ca/science/white_papers/eHiTS_on_the_Cell.pdf) > > Best regards, > Aniko Simon > -- > VP Business Development > SimBioSys Inc. > www.simbiosys.ca> > -- ================================= A. Geoffrey Skillman, MD PhD Vice President, Research OpenEye Scientific Software, Inc. skillman * eyesopen.com www.eyesopen.com From owner-chemistry@ccl.net Mon Jan 28 17:13:00 2008 From: "Elaine Meng meng[a]cgl.ucsf.edu" To: CCL Subject: CCL: NIH NCRR booth at Biophysical Society 2008 Message-Id: <-36132-080128135655-21280-/47SVbVlW0Owfqbu9tJ+Jg[#]server.ccl.net> X-Original-From: "Elaine Meng" Date: Mon, 28 Jan 2008 13:56:51 -0500 Sent to CCL by: "Elaine Meng" [meng a cgl.ucsf.edu] The NIH National Center for Research Resources (NCRR) will be hosting booth #719 at the Biophysical Society Meeting 2008 (Feb 2-6, Long Beach, CA) http://www.biophysics.org/meetings/2008/ http://www.cgl.ucsf.edu/events/BPS2008/ Presentations cover recent work in structure determination and software such as NAMD, VMD, UCSF Chimera, Gfit, and Virtual Cell. Booth schedule: -------------- Sunday Feb 3 10 am The Structure-Function Linkage Database: A resource for exploring enzyme superfamilies (RBVI: Shoshana Brown) 11 am Cryo-EM of Molecular Machines at 0.4 nm Resolution (NCMI: Htet Khant) 12 pm Intro to UCSF Chimera molecular modeling package (RBVI: Scooter Morris) 1 pm Resource for Visualization of Biological Complexity: Applications to Ryanodine Receptor (RVBC: Terence Wagenknect) Determining the structure of the calcium release unit within triad junctions by cryo-electron tomography (RVBC: Christian Renken) 2 pm New Features in UCSF Chimera (RBVI: Elaine Meng, Eric Pettersen) 3 pm Using electron tomography to define function-linked remodelings of the mitochondrial inner membrane: Apoptosis and oxidative stress (RVBC: Carmen Mannella) Classification of heterogeneous data sets in single-particle reconstruction (RVBC: Joachim Frank) 4 pm structureViz: Linking Cytoscape to Chimera (RBVI: Scooter Morris) -------------- Monday Feb 4 10 am Virtual Cell: Tutorial in new capabilities (NRCAM: Ion I. Moraru) 11 am National Resource for Automated Molecular Microscopy (NRAMM: Neil Vossman) 12 pm Resources for teaching quantitative cell biology at undergraduate and graduate levels (NRCAM: Raquell Holmes) 1 pm Gfit Demo: Universal Approach to global fitting of data from multiple types of experiments to computational models (NRCAM: Mikhail Levin) 2 pm Using Virtual Cell to generate and explore quantitative model of actin polymerization at the leading edge of cells (NRCAM: Les Loew) 3 pm National Resource for Automated Molecular Microscopy (NRAMM: Pick-Wei La) 4 pm Using Virtual Cell to explore quantitative models of PIP2 signaling in Cerebellar Purkinje Spines (NRCAM: Sherry Ann Brown) -------------- Tuesday Feb 5 11 am Visualizing 3-D Electron Microscopy Data with UCSF Chimera (RBVI: Tom Goddard) 12 pm Resource for Biocomputing, Visualization, and Informatics (RBVI: Tom Ferrin) 1 pm National Resource for Automated Molecular Microscopy (NRAMM: Gabe Lander) 3 pm National Resource for Automated Molecular Microscopy (NRAMM: Anke Mulder) 4 pm Exploring Biomolecular Machines with NAMD and VMD (RMMB: Yi Wang) -------------- From owner-chemistry@ccl.net Mon Jan 28 17:47:00 2008 From: "zborowsk+/-chemia.uj.edu.pl" To: CCL Subject: CCL:G: problem with aim calculation. Message-Id: <-36133-080128142125-330-sfdnNtxHobyD4rTIjrVxvw##server.ccl.net> X-Original-From: zborowsk**chemia.uj.edu.pl Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-2 Date: Mon, 28 Jan 2008 18:16:06 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: zborowsk-x-chemia.uj.edu.pl Hi Try AIMPAC, its free and good (there are also Morphy and AIM2000 but they are not free) I have not tried to perform the AIM analysis in Gaussian so far because all my "AIM teachers" always said that at this point Gaussian is useless. regards Kzys > > Sent to CCL by: "abdeladim guermoune" [lguermoune,hotmail.com] > Dear members, > I try to run a calculation in G03 with aim instructions > To find a critical points for geometries including > Iron and bridged hydrogen between borons atoms (tree centers two > electrons) > But I get de following message in the end of the output file: > > THE MOLECULAR GRAPH IS DISCONNECTED ... ABORTING! > Error termination via Lnk1e in /users/g03/l609.exe at Sun Jan 27 23:33:36 > 2008. > > > I used as keywords in the input file: > > #p B3P86 6-311++G(3df,2p) aim=all density=current scf=(tight,save) > output=wfn scfcyc=250 guess=huckel > > Can any one have suggestions to result this problem? > (sorry for my English, its the third foreigner language for me) > Yours, > > ----------------------------------- > GUERMOUNE Abdeladim. > University Cadi Ayyad > Morocco.> > > -- Krzysztof Zborowski Faculty of Chemistry Jagiellonian University 3 Ingardena Street 30-060 Krakow Poland phone: +48(12)632-4888 ext. 2064 or 2067 fax: +48(12)634-05-15 email: zborowsk(0)chemia.uj.edu.pl ICQ 158385743 gg 3817259 skype kzys70 From owner-chemistry@ccl.net Mon Jan 28 18:22:01 2008 From: "=?ISO-8859-1?Q?Sina_T=FCreli?= sinatureli ~ gmail.com" To: CCL Subject: CCL: Computational Spectroscopy Message-Id: <-36134-080128173159-18392-vVbHBel6tzNtxpHD/CYtqA~~server.ccl.net> X-Original-From: "=?ISO-8859-1?Q?Sina_T=FCreli?=" Content-Type: multipart/alternative; boundary="----=_Part_18683_672975.1201557496097" Date: Mon, 28 Jan 2008 23:58:16 +0200 MIME-Version: 1.0 Sent to CCL by: "=?ISO-8859-1?Q?Sina_T=FCreli?=" [sinatureli^-^gmail.com] ------=_Part_18683_672975.1201557496097 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline I just wanted to bring up my question once more to see if anybody has an answer On Jan 23, 2008 11:49 AM, Sina T reli sinatureli[#]gmail.com < owner-chemistry^_^ccl.net> wrote: > > Sent to CCL by: "Sina T reli" [sinatureli ~ gmail.com] > Hello, > > I have some questions regarding computational spectroscopy. My aim is to > find the spectral orbital overlap between some molecules (namely > chlorophylls). I use arguslab to produce the transition wavelengths and use > a homogenous linewidth of 2nm to produce graphs of absorption with width. > However I need a method for determining also their emission spectra and for > that since they are quite immobile in their enviroment a mirror image about > the 0->0 transition is suggested in some literatures and books. My question > is is there a way in which I can find where in the graph is this 0->0 > transition is supposed to be. I know it is near the end but since I am going > to calculate spectral overlap of molecules, I need a more precise way of > finding it.. Or is there any tool that will produce the emission spectra of > molecules? > > Second question comes to users of arguslab. When a spectral analysis is > done on the molecule at any given transition dipole electric length and > state dipole length. Are these measured in debye or do they just give the > directions of the dipoles. If I am looking for the magnitute of transition > dipole moment of any given transition, is the length of this transition > dipole electric length that will give me the value? > > Thanks in advance for your answers.> > > ------=_Part_18683_672975.1201557496097 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline I just wanted to bring up my question once more to see if anybody has an answer

On Jan 23, 2008 11:49 AM, Sina T reli sinatureli[#]gmail.com <owner-chemistry^_^ccl.net> wrote:

Sent to CCL by: "Sina  T  reli" [sinatureli ~ gmail.com]
Hello,

I have some questions regarding computational spectroscopy. My aim is to find the spectral orbital overlap between some molecules (namely chlorophylls). I use arguslab to produce the transition wavelengths and use a homogenous linewidth of 2nm to produce graphs of absorption with width. However I need a method for determining also their emission spectra and for that since they are quite immobile in their enviroment a mirror image about the 0->0 transition is suggested in some literatures and books. My question is is there a way in which I can find where in the graph is this 0->0 transition is supposed to be. I know it is near the end but since I am going to calculate spectral overlap of molecules, I need a more precise way of finding it.. Or is there any tool that will produce the emission spectra of molecules?

Second question comes to users of arguslab. When a spectral analysis is done on the molecule at any given transition dipole electric length and state dipole length. Are these measured in debye or do they just give the directions of the dipoles. If I am looking for the magnitute of transition dipole moment of any given transition, is the length of this transition dipole electric length that will give me the value?

Thanks in advance for your answers.



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------=_Part_18683_672975.1201557496097-- From owner-chemistry@ccl.net Mon Jan 28 18:59:00 2008 From: "Jochen Heil jheil^_^keychem.de" To: CCL Subject: CCL:G: Gaussian: Saving/reading 1-electron integrals to/from disk Message-Id: <-36135-080128172936-17355-TvREznn3QXqVEkOlQKy07Q*_*server.ccl.net> X-Original-From: "Jochen Heil" Date: Mon, 28 Jan 2008 17:29:32 -0500 Sent to CCL by: "Jochen Heil" [jheil=-=keychem.de] Dear computational chemists, i want to do a (quite long) series of single point energy calculations in the presence of different charge backgrouds represented by point charges (140 points in each direction). In previous calculations i have come to believe that the rate determining step of this type of calculation is the computation of the integrals (most of the calculation time is used by link 302). If my assumptions are correct, then the reason for this is that each point charge is essentially treated as if it was a nucleus, which means that the integral has the same form as the (1-electron)-nuclear attraction integrals, and the total number of these integrals is 140 + number of atoms. Since the charge at a given point on the grid is a constant, it should be possible to move it in front of the integral, which would then only depend on the position of the point charge, and it would be possible to compute these integrals only once and read them from file for each computation (faster than recomputaion?). Unfortunately as far as i have seen, Gaussian only saves the 2-electron integrals to disk (via checkpoint- or 2-electron-integral-file). Did I miss anything in the manual? Do I have to modify the program? I am looking forward to any suggestions... Jochen Heil, Diploma student, Darmstadt University of Technology From owner-chemistry@ccl.net Mon Jan 28 19:33:00 2008 From: "Aniko Simon aniko[]simbiosys.ca" To: CCL Subject: CCL: LASSO paper and SimBioSys blog Message-Id: <-36136-080128182545-27306-f/1wLbKI6HNCQJSswNteEQ---server.ccl.net> X-Original-From: "Aniko Simon" Date: Mon, 28 Jan 2008 18:25:41 -0500 Sent to CCL by: "Aniko Simon" [aniko]*[simbiosys.ca] Geoff, Thanks for the invitation to participate. I found out about this on Friday of last week with the news wire release. It looks very interesting but it is extremely short notice with a mid-February deadline as I read it. I made a blog posting about this and have tried to spread the awareness within the community on your behalf (http://www.simbiosys.ca/blog/2008/01/26/are-you-aware-of-sampl/). I found that it was announced on the SAMPL page on November 1st of last year but don't recall seeing it announced on CCL. That's a great shame as we could have had time to schedule our participation. I'll follow up with you offline about our participation and who else is involved etc. as I can't see a list of participants on the page. Thanks for the invite. Aniko On Monday 28 January 2008 15:19, Geoff Skillman skillman,,eyesopen.com wrote: > Sent to CCL by: Geoff Skillman [skillman=eyesopen.com] > Dear Aniko- > > Perhaps you should apply your new technology to the "Statistical > Assessment of the Modeling of Proteins and Ligands" (SAMPL). It is a > blinded trial of virtual screening, pose-prediction and affinity > prediction based on proprietary data from Abbott Laboratories and Vertex > Pharmaceuticals. Several academic groups and software vendors from the > virtual screening field are participating. It would be a good > opportunity to demonstrate how LASSO compares to other virtual screening > methods. > > You can sign up for the evaluation and get further details at > http://sampl.eyesopen.com > > SAMPL also includes a blinded transfer energy prediction data set. > > Best Regards, > Geoff Skillman > > Aniko Simon aniko ~~ simbiosys.ca wrote: > > Sent to CCL by: "Aniko Simon" [aniko/a\simbiosys.ca] > > SimBioSys would like to make two announcements: > > > > 1) Our publication regarding "LASSO-ligand activity by surface similarity > > order: a new tool for ligand based virtual screening" has just been > > published in the Journal of Computer-Aided Molecular Design and is > > available at this link: http://dx.doi.org/10.1007/s10822-007-9164-5. > > LASSO is a ligand-based similarity search tool that uses surface > > properties of known active molecules to build a model for screening large > > databases for molecules with similar properties. The tool is extremely > > fast and can screen a database of a million molecules in under 1 minute > > on a standard single CPU machine. LASSO is independent of the underlying > > 2D skeleton or the 3D conformation and has the ability to retrieve > > molecules with very different 2D scaffolds (chemotypes) without the need > > for a bioactive conformation. > > > > LASSO is the basis of exciting work presently underway with ChemSpider > > (www.chemspider.com). We have teamed up to provide the virtual screening > > results for 40 target families on the full ChemSpider Library, currently > > containing over 18 million molecules. Using the LASSO similarity search > > tool, SimBioSys has screened the ChemSpider database against all 40 > > target families from the Database of Useful Decoys (DUD) dataset. The > > work is discussed in a little more detail on their blog at > > http://www.chemspider.com/blog/announcing-the-chemspider-ligand-activity- > >project-partnering-with-simbiosys.html. We will also cover the > > developments at http://www.simbiosys.ca/lasso/publications.html > > > > > > 2) The SimBioSys blog is now online: http://www.simbiosys.ca/blog/. The > > purpose behind this blog has already been discussed in the opening > > blogpost > > (http://www.simbiosys.ca/blog/2008/01/09/welcome-hello-world-lets-begin-t > >he-discussion/). We look forward to engaging scientists in active > > discussions on our blog and keeping everyone updated with our > > developments, specifically our work to utilize high performance computing > > for the purpose of accelerated docking (see the White Paper > > http://www.simbiosys.ca/science/white_papers/eHiTS_on_the_Cell.pdf) > > > > Best regards, > > Aniko Simon > > -- > > VP Business Development > > SimBioSys Inc. > > www.simbiosys.ca> From owner-chemistry@ccl.net Mon Jan 28 20:07:00 2008 From: "Close, David M. CLOSED,+,mail.etsu.edu" To: CCL Subject: CCL:G: memory problem in Gaussian Message-Id: <-36137-080128182129-24052-qAqr/j2YqMV0PfJ8v0t9Ng-.-server.ccl.net> X-Original-From: "Close, David M." Content-class: urn:content-classes:message Content-Type: multipart/mixed; boundary="----_=_NextPart_001_01C86204.7B61D7A0" Date: Mon, 28 Jan 2008 18:18:05 -0500 MIME-Version: 1.0 Sent to CCL by: "Close, David M." [CLOSED.\a/.mail.etsu.edu] This is a multi-part message in MIME format. ------_=_NextPart_001_01C86204.7B61D7A0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Let me first ask a trivial question. When you allocate rwf memory, have = you looked at the directory to see if the files are actually full? If = so, try adding more. You can add 5 more 2mb blocks. =20 If that doesn't work, there are versions of G03 that have solved this 32 = bit limitaion. This was described on the CCL site a week or so ago. ________________________________ > From: Alexander Hoepker achoepker:+:gmail.com = [mailto:owner-chemistry\a/ccl.net] Sent: Mon 1/28/2008 2:18 PM To: Close, David M. Subject: CCL:G: memory problem in Gaussian I'm running out of memory during one of my transition state calculation = in Gaussian 03. Even though the atom size is smaller than others that = have worked before, the computer runs out of memory during its initial = frequency calculation. I tried to solve this issue in three ways:=20 (1) restrict the three atoms that are described by the imaginary = frequency, optimize this and resubmit to an unconstrained TS = calculation. (2) solve the memory issue by splitting the file into five chunks = (r1-r5) each being slightly less than 2GB (250MW). usr2/GAUSS_SCR is = the scratch directory. I'm using a 32 bit computer. %RWF=3D/usr2/GAUSS_SCR/r1,249MW,/usr2/GAUSS_SCR/r2,249MW,/usr2/ GAUSS_SCR/r3,249MW,/usr2/GAUSS_SCR/r4,249MW,/usr2/GAUSS_SCR/r5 ,249MW Both approaches fail by crashing at the frequency calculation. Does = anyone have a suggestion? Thanks is advance ------_=_NextPart_001_01C86204.7B61D7A0-- From owner-chemistry@ccl.net Mon Jan 28 23:40:00 2008 From: "Yangsoo Kim vsmember%x%gmail.com" To: CCL Subject: CCL:G: PC-Gamess DFT Setting? Message-Id: <-36138-080128230702-27491-m6VWmdFjB/aCbWohtgqdOA##server.ccl.net> X-Original-From: "Yangsoo Kim" Content-Type: multipart/alternative; boundary="----=_Part_13078_18016022.1201575858880" Date: Tue, 29 Jan 2008 12:04:18 +0900 MIME-Version: 1.0 Sent to CCL by: "Yangsoo Kim" [vsmember|gmail.com] ------=_Part_13078_18016022.1201575858880 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear CCL members, I am fairly new for Gamess. Currently, I am using the PC-Gamess 7.1.5(Patched). I want to calculate DFT energy, frequency and raman intensity by using PC-Gamess. I used the g03 keywords (#B3LYP/6-31G(d) opt freq=raman) for the above calculations. Can you recommend $DFT keyword settings of PC-Gamess corresponding to g03 default options (convergence criteria, opt. stepsize, etc...)? And I have another question... Please give me the example for runtyp=raman calculation. Sincerely, Yangsoo Kim ------=_Part_13078_18016022.1201575858880 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Dear CCL members,
 
I am fairly new for Gamess. Currently, I am using the PC-Gamess 7.1.5 (Patched).
 
I want to calculate DFT energy, frequency and raman intensity by using PC-Gamess.
 
I used the g03 keywords (#B3LYP/6-31G(d) opt freq=raman) for the above calculations.
 
Can you recommend $DFT keyword settings of PC-Gamess corresponding to g03 default options (convergence criteria, opt. stepsize, etc...)?
 
And I have another question...
 
Please give me the example for runtyp=raman calculation.
 
Sincerely,
 
 
Yangsoo Kim
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