From owner-chemistry@ccl.net Thu Apr 22 10:37:00 2010 From: "xunlei ding dingxunlei[a]gmail.com" To: CCL Subject: CCL: [GaussView] How to save the preferences to a file? Message-Id: <-41688-100422102953-30810-C0Vm9+15bPTuy9HbyStPPg^-^server.ccl.net> X-Original-From: xunlei ding Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=GB2312 Date: Thu, 22 Apr 2010 22:29:44 +0800 MIME-Version: 1.0 Sent to CCL by: xunlei ding [dingxunlei{}gmail.com] Hi, Jamin, Thank you very much! It is really difficuly to find the analogous file to "gaussview5rc" in Wind= ows. Can anybody give me additional help on this problem? 2010/4/19 xunlei ding dingxunlei,+,gmail.com : > > Sent to CCL by: xunlei ding [dingxunlei(~)gmail.com] > Dear All, > > Can the preferences of GaussView to be saved to a file, so I can > reload it on a different computer? > It is known that the "default" preferences can be reloaded. > But how about the customed one? > > Thank you very much! > > Ding > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 ------------------------------------------------------ Xun-Lei Ding (=B6=A1=D1=B8=C0=D7) From owner-chemistry@ccl.net Thu Apr 22 11:16:00 2010 From: "Tina Kamma Lorger KammaCS=cf.ac.uk" To: CCL Subject: CCL: ZDOCK Message-Id: <-41689-100422095711-31111-nqmQoTyoRs2cpFWeBFFaHw__server.ccl.net> X-Original-From: "Tina Kamma Lorger" Date: Thu, 22 Apr 2010 09:57:10 -0400 Sent to CCL by: "Tina Kamma Lorger" [KammaCS]~[cf.ac.uk] I downloaded ZDOCK in Linux Ubuntu and it seems to be running OK. However, I cannot get the mark_sur program to work (mark_sur prot.pdb prot1.pdb). Does anybody know what I can possibly be doing wrong please? T From owner-chemistry@ccl.net Thu Apr 22 11:51:00 2010 From: "Lorenzo Ferro L.Ferro ~ sussex.ac.uk" To: CCL Subject: CCL:G: 4333111/433111/43 basis set calculation on Gaussian Message-Id: <-41690-100422104402-15731-fCXFnLaGUOcxVY3OwlqzjQ:_:server.ccl.net> X-Original-From: "Lorenzo Ferro" Date: Thu, 22 Apr 2010 10:44:01 -0400 Sent to CCL by: "Lorenzo Ferro" [L.Ferro[#]sussex.ac.uk] Thanks to everyone for the useful answers. I resume down here the answers: -The basis set needed comes from the book "Gaussian Basis Sets for Molecular Calculations" by S. Huzinaga and coworkers. The notation is explained in, e.g., J. of Comput. Chem. 5, 146-161 (1984), and is illustrated in the input for SnCl4: 0 1 Sn Cl 1 R Cl 1 R 2 T Cl 1 R 2 T 3 T 1 Cl 1 R 2 T 3 T -1 R=2.280 T=109.47122063 Sn 0 s 4 1.00 37472.012 0.16625195E-01 5648.8845 0.11693876 1282.9402 0.43179058 346.45090 0.56561483 s 3 1.00 516.78654 -0.11389480 59.928116 0.64603107 26.048741 0.42625579 s 3 1.00 47.977453 -0.27270744 8.7546722 0.84987426 4.0102331 0.30296902 s 3 1.00 7.5198796 0.34211658 1.7271022 -0.80241707 0.77274433 -0.40406798 s 1 1.00 1.1386522 -0.20454514 s 1 1.00 0.17346487 0.71113158 s 1 1.00 0.66274942E-01 0.41257362 p 4 1.00 1745.5260 0.24426685E-01 410.51366 0.16656335 128.31139 0.49415429 44.903462 0.47526995 p 3 1.00 140.77605 -0.24768418E-01 18.242647 0.47906186 7.1374774 0.58978085 p 3 1.00 2.9465525 0.42389675 1.2795029 0.53117256 0.54560639 0.12762194 p 1 1.00 0.25902160 0.33944667 p 1 1.00 0.10239424 0.54968903 p 1 1.00 0.41491833E-01 0.21901539 d 4 1.00 201.37580 0.39987711E-01 58.454606 0.22658972 20.557877 0.52423023 7.4534071 0.42264248 d 3 1.00 4.6147167 0.27827403 1.6488579 0.56541336 0.56081639 0.34880807 d 1 1.00 0.253 1.0 d 1 1.00 0.078 1.0 **** Cl 0 6-31G* **** - For directions on how to enter a general basis: http://glab.cchem.berkeley.edu/glab/faqs/gauss_custombasis.html Thanks again! Lorenzo > "Lorenzo Ferro L.Ferro]*[sussex.ac.uk" wrote: > > Sent to CCL by: "Lorenzo Ferro" [L.Ferro ~~ sussex.ac.uk] > The question might look silly, I am trying to run a single point energy calculation on Gaussian 03 using the [4333111/433111/43] basis set for the Sn atom, how do I have to set up the input file to use this basis set? Moreover, how do I add the polarization function for it? > > I thought that putting b3lyp/gen in the rout card and specifying > > Sn 0 > 4333111/433111/43 > **** > C H N O > 6-31G* > **** > > at the end would be ok, but apparently it is not... > > Thank you!!! > > Lorenzo > > > ---------------------------- > Lorenzo Ferro > PhD Student > University of Sussex > BN1 9QJ Brighton UK > email: L.Ferro[a]sussex.ac.uk > ---------------------------- > > From owner-chemistry@ccl.net Thu Apr 22 12:26:01 2010 From: "DIEGOI GOMEZ darkego21 ~ yahoo.com" To: CCL Subject: CCL: Error termination in NtrErr at MP2 calculation. Message-Id: <-41691-100422105615-5918-qohBWnZLWN1gX2CvNlL6Yw{}server.ccl.net> X-Original-From: DIEGOI GOMEZ Content-Type: multipart/alternative; boundary="0-218494364-1271944568=:94060" Date: Thu, 22 Apr 2010 06:56:08 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: DIEGOI GOMEZ [darkego21+/-yahoo.com] --0-218494364-1271944568=:94060 Content-Type: text/plain; charset=us-ascii Hello there. I'm doing an optimization of a pair of interacting molecules at MP2 level with simultaneous counterpoise correction. I'm using two basis set (lanl2dz and 6-31G**) through the "GEN" keyword. The calculation starts without problems, so the first SCF cycle and the second-order perturbation are accomplished. However, when the next step starts the follow Error is reported: --------------------------------------------------------------------------------------------------------------------------------------------- ***** Axes restored to original set ***** Cartesian Forces: Max 0.199455160 RMS 0.055013514 Operation on file out of range. FileIO: IOper= 2 IFilNo(1)= -522 Len= 118 IPos= 118 Q= 47965310131088 dumping /fiocom/, unit = 1 NFiles = 98 SizExt = 524288 WInBlk = 512 defal = T LstWrd = 233431552 FType=2 FMxFil=10000 Number 0 0 0 0 0 0 0 0 Base 12203972 390144 495616 321536 12752384 10698752 201216 365568 End 12204032 402432 527360 322048 12818944 11614208 201728 372736 End1 12204032 402432 527360 322048 12818944 11614208 201728 372736 Wr Pntr 12203972 388608 495616 321536 12533760 10698752 201216 365568 Rd Pntr 12203972 388608 495616 321536 12533760 10698752 201216 365568 Length 60 12288 31744 512 66560 915456 512 7168 (...) Error termination in NtrErr: NtrErr Called from FileIO. ---------------------------------------------------------------------------------------------------------------------------------------------- Thanks in advance for any sugestion. Diego UPV-ITQ Spain. --0-218494364-1271944568=:94060 Content-Type: text/html; charset=us-ascii
Hello there.

I'm doing an optimization of a pair of interacting molecules at MP2 level with simultaneous counterpoise correction. I'm using two basis set (lanl2dz and 6-31G**) through the "GEN" keyword.  The calculation starts without problems, so the first SCF cycle and the second-order perturbation are accomplished. However, when the next step starts the follow Error is reported:

---------------------------------------------------------------------------------------------------------------------------------------------
  ***** Axes restored to original set *****
 Cartesian Forces:  Max     0.199455160 RMS     0.055013514
 Operation on file out of range.
FileIO: IOper= 2 IFilNo(1)=  -522 Len=         118 IPos=         118 Q=   47965310131088


 dumping /fiocom/, unit = 1 NFiles =    98 SizExt =    524288 WInBlk =       512
                   defal = T LstWrd =   233431552 FType=2 FMxFil=10000

 Number           0          0          0          0          0          0          0          0
 Base      12203972     390144     495616     321536   12752384   10698752     201216     365568
 End       12204032     402432     527360     322048   12818944   11614208     201728     372736
 End1      12204032     402432     527360     322048   12818944   11614208     201728     372736
 Wr Pntr   12203972     388608     495616     321536   12533760   10698752     201216     365568
 Rd Pntr   12203972     388608     495616     321536   12533760   10698752     201216     365568
 Length          60      12288      31744        512      66560     915456        512       7168

(...)

 Error termination in NtrErr:
 NtrErr Called from FileIO.

----------------------------------------------------------------------------------------------------------------------------------------------

Thanks in advance for any sugestion.

Diego
UPV-ITQ
Spain.


--0-218494364-1271944568=:94060-- From owner-chemistry@ccl.net Thu Apr 22 14:06:00 2010 From: "Close, David M. CLOSED_._mail.etsu.edu" To: CCL Subject: CCL: Error termination in NtrErr at MP2 calculation. Message-Id: <-41692-100422140237-22018-oiVVbgUq5mRy/5YzCcHa4g- -server.ccl.net> X-Original-From: "Close, David M." Content-Class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01CAE245.F4C2DF65" Date: Thu, 22 Apr 2010 14:02:19 -0400 MIME-Version: 1.0 Sent to CCL by: "Close, David M." [CLOSED()mail.etsu.edu] ------_=_NextPart_001_01CAE245.F4C2DF65 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable Diegoi: This is a common error that means you have exceeded disc storage space. This happens with MP2 calculations that requires a great deal of scratch disc space for storing integrals. There are common fixes to this problem, but it is necessary to tell us about the size of the calculation you are doing. Like how many heavy atoms, and what program you are using. Basically a 32 bit machine is limited to 16 Gbytes of storage. Have you tried simple fixes like %rwf=3D .... ? Regards, Dave Close. =20 > From: owner-chemistry+closed=3D=3Detsu.edu^^^ccl.net [mailto:owner-chemistry+closed=3D=3Detsu.edu^^^ccl.net] On Behalf Of = DIEGOI GOMEZ darkego21 ~ yahoo.com Sent: Thursday, April 22, 2010 9:56 AM To: Close, David M. Subject: CCL: Error termination in NtrErr at MP2 calculation. =20 Hello there. I'm doing an optimization of a pair of interacting molecules at MP2 level with simultaneous counterpoise correction. I'm using two basis set (lanl2dz and 6-31G**) through the "GEN" keyword. The calculation starts without problems, so the first SCF cycle and the second-order perturbation are accomplished. However, when the next step starts the follow Error is reported: ------------------------------------------------------------------------ --------------------------------------------------------------------- ***** Axes restored to original set ***** Cartesian Forces: Max 0.199455160 RMS 0.055013514 Operation on file out of range. FileIO: IOper=3D 2 IFilNo(1)=3D -522 Len=3D 118 IPos=3D = 118 Q=3D 47965310131088 dumping /fiocom/, unit =3D 1 NFiles =3D 98 SizExt =3D 524288 = WInBlk =3D 512 defal =3D T LstWrd =3D 233431552 FType=3D2 = FMxFil=3D10000 Number 0 0 0 0 0 0 0 0 Base 12203972 390144 495616 321536 12752384 10698752 201216 365568 End 12204032 402432 527360 322048 12818944 11614208 201728 372736 End1 12204032 402432 527360 322048 12818944 11614208 201728 372736 Wr Pntr 12203972 388608 495616 321536 12533760 10698752 201216 365568 Rd Pntr 12203972 388608 495616 321536 12533760 10698752 201216 365568 Length 60 12288 31744 512 66560 915456 512 7168 (...) Error termination in NtrErr: NtrErr Called from FileIO. ------------------------------------------------------------------------ ---------------------------------------------------------------------- Thanks in advance for any sugestion. Diego UPV-ITQ Spain. =20 ------_=_NextPart_001_01CAE245.F4C2DF65 Content-Type: text/html; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable

Diegoi:

  This is a common error that means you have = exceeded disc storage space.  This happens with MP2 calculations that requires a great = deal of scratch disc space for storing integrals.  There are common fixes = to this problem, but it is necessary to tell us about the size of the = calculation you are doing.  Like how many heavy atoms, and what program you are using.  Basically a 32 bit machine is limited to 16 Gbytes of = storage.  Have you tried simple fixes like %rwf=3D   …. = ?

  Regards, Dave Close.

 

From:= owner-chemistry+closed=3D=3Detsu.edu^^^ccl.net [mailto:owner-chemistry+closed=3D=3Detsu.edu^^^ccl.net] On Behalf Of = DIEGOI GOMEZ darkego21 ~ yahoo.com
Sent: Thursday, April 22, 2010 9:56 AM
To: Close, David M.
Subject: CCL: Error termination in NtrErr at MP2 = calculation.

 

Hello there.

I'm doing an optimization of a pair of interacting molecules at MP2 = level with simultaneous counterpoise correction. I'm using two basis set (lanl2dz = and 6-31G**) through the "GEN" keyword.  The calculation = starts without problems, so the first SCF cycle and the second-order = perturbation are accomplished. However, when the next step starts the follow Error is = reported:

-------------------------------------------------------------------------= --------------------------------------------------------------------
  ***** Axes restored to original set *****
 Cartesian Forces:  Max     0.199455160 RMS     0.055013514
 Operation on file out of range.
FileIO: IOper=3D 2 IFilNo(1)=3D  -522 Len=3D         118 IPos=3D         118 = Q=3D   47965310131088


 dumping /fiocom/, unit =3D 1 NFiles =3D    98 = SizExt =3D    524288 WInBlk = =3D       512
            &= nbsp;      defal =3D T LstWrd =3D   233431552 FType=3D2 = FMxFil=3D10000

 Number           0          0          0          = 0          0          0          0          0
 Base      = 12203972     390144     495616     321536   12752384   10698752     201216     365568
 End       = 12204032     402432     527360     322048   12818944   11614208     201728     372736
 End1      = 12204032     402432     527360     322048   12818944   11614208     = 201728     372736
 Wr Pntr   12203972     388608     495616     321536   12533760   10698752     201216     365568
 Rd Pntr   12203972     388608     495616     321536   12533760   10698752     201216     365568
 Length          60      12288      31744        512      66560     915456        512       7168

(...)

 Error termination in NtrErr:
 NtrErr Called from FileIO.

-------------------------------------------------------------------------= ---------------------------------------------------------------------
=
Thanks in advance for any sugestion.

Diego
UPV-ITQ
Spain.

 

------_=_NextPart_001_01CAE245.F4C2DF65-- From owner-chemistry@ccl.net Thu Apr 22 16:01:00 2010 From: "Jason D Biggs jbiggs2%a%uoregon.edu" To: CCL Subject: CCL:G: PES scan on excited state - G09 Message-Id: <-41693-100422143438-14908-pwHVnsQ1wdUfLvs+wm89Fg(_)server.ccl.net> X-Original-From: "Jason D Biggs" Date: Thu, 22 Apr 2010 14:34:36 -0400 Sent to CCL by: "Jason D Biggs" [jbiggs2|,|uoregon.edu] I am trying to get PESs for both the ground electronic state, and first excited states as a function of some internal coordinate. It is pretty simple to get the ground state curve using the "scan" keyword. I can change the basis set used to do the scan, and even choose between HF or DFT or MP2. But when I set the method to CIS(root=1) instead of HF (which, unless I am mistaken, is all I need to do for an opt or freq job to get information on the S1 state instead of the ground state), I don't get a different PES at all. It seems that Gaussian instead finds all the excited states first, then does the scan for the ground state. Is there any way to get Gaussian to do the scan for the first excited singlet state? It seems like a pretty common calculation type - I often see Born-Oppenheimer surfaces for multiple electronic states. If this isn't possible, I could imagine doing it myself by making a series of Gaussian input files that simply found the energy of the first excited state for a given molecular geometry - but the method I'd use to do this probably wouldn't be the most efficient way. Thanks in advance Jason Biggs University of Oregon From owner-chemistry@ccl.net Thu Apr 22 16:36:00 2010 From: "Ashish D ashish.ashrock-.-gmail.com" To: CCL Subject: CCL:G: Question regarding geometry optimization Message-Id: <-41694-100422131224-30253-XkVvko+N4sBQ+5McTisWnA() server.ccl.net> X-Original-From: "Ashish D" Date: Thu, 22 Apr 2010 13:12:22 -0400 Sent to CCL by: "Ashish D" [ashish.ashrock ~~ gmail.com] Hello All I am getting the error message in my geometry optimization. The optimization is carried out at HF/6-31+G(d,p) of a T12 cluster of zeolite Y. I am getting the following error message : Small interatomic distances encountered: 2 1 3 1 3 2 4 1 4 2 4 3 5 1 5 2 5 3 5 4 6 1 6 2 6 3 6 4 6 5 7 1 7 2 7 3 7 4 7 5 Problem with the distance matrix. Error termination via Lnk1e in /usr/local/g03/l202.exe Any help and suggestions will be appreciated. Thanks, A From owner-chemistry@ccl.net Thu Apr 22 17:10:00 2010 From: "Deepangi Pandit deepangi.pandit-,-gmail.com" To: CCL Subject: CCL: ZDOCK Message-Id: <-41695-100422131402-31198-x+HMItjyOYl2w3JCUmPTjg{}server.ccl.net> X-Original-From: Deepangi Pandit Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 22 Apr 2010 12:16:17 -0400 MIME-Version: 1.0 Sent to CCL by: Deepangi Pandit [deepangi.pandit^^^gmail.com] Hi Tinna: Generally mark_sur will not work of following reasons 1. Your input files are too close to each other - You can fix these by trying different initial orientations of two proteins 2. You are using homology models and models are not optimized - refine your homology models All the best. Deepa On Thu, Apr 22, 2010 at 9:57 AM, Tina Kamma Lorger KammaCS=3Dcf.ac.uk wrote: > > Sent to CCL by: "Tina =A0Kamma Lorger" [KammaCS]~[cf.ac.uk] > I downloaded ZDOCK in Linux Ubuntu and it seems to be running OK. However= , I cannot get the mark_sur program to work (mark_sur prot.pdb prot1.pdb). = Does anybody know what I can possibly be doing wrong please? > T > > > > -=3D This is automatically added to each message by the mailing script = =3D-> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml> =A0 =A0 =A0http://www.ccl.net/spammers.txt> > > From owner-chemistry@ccl.net Thu Apr 22 17:45:00 2010 From: "Kelly 8D i.m.smilin.kelly]_[gmail.com" To: CCL Subject: CCL: TINKER sovation with polar molecules Message-Id: <-41696-100422150713-22835-oeEqXTleQjruy5Zunf97dA===server.ccl.net> X-Original-From: Kelly 8D Content-Type: multipart/alternative; boundary=000e0cd10622abe6970484d735de Date: Thu, 22 Apr 2010 11:09:20 -0700 MIME-Version: 1.0 Sent to CCL by: Kelly 8D [i.m.smilin.kelly%gmail.com] --000e0cd10622abe6970484d735de Content-Type: text/plain; charset=ISO-8859-1 Hi CCL users! I am trying to solvate a small molecule in water using TINKER. I have searched the archives, and found references to xyzedit and soak. I don't have soak, so am using xyzedit. When generating the water with xyzedit (option 16), the water box contains water molecules that are all aligned in the same direction. So when I try to minimize, optimize, or Newton the xyz file, to relax it into something i can do MD on, the program crashes with: INDUCE -- Warning, Induced Dipoles are not Converged TINKER is Unable to Continue; Terminating the Current Calculation I find that small systems (~<30 waters) will run - probably because the system as a whole has less dipole moment - but I know most users are making bigger boxes than that... How are you relaxing the system enough to do MD? If you prefer to reply in person, e-mail is kelly.theel|-|email.ucr.edu Thanks for any help you can give! -- - Kelly "Most folks are about as happy as they make up their minds to be." - Abraham Lincoln --000e0cd10622abe6970484d735de Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hi CCL users!
=A0
I am trying to solvate a small molecule in water using TINKER.=A0 I ha= ve searched the archives, and found references to xyzedit and soak.=A0 I do= n't have soak, so am using xyzedit.
=A0
When generating the water with xyzedit (option 16), the water box cont= ains water molecules that are all aligned in the same direction.=A0 So when= I try to minimize, optimize, or Newton the xyz file, to relax it into some= thing i can do MD on, the program crashes with:
=A0
=A0
INDUCE=A0 =A0--=A0=A0 Warning, Induced Dipoles are not Converged
TINKER is Unable to Continue; Terminating the Current Calculation
=A0
=A0
I find that small systems (~<30 waters) will run - probably because= the system as a whole has less dipole moment - but I know most users are m= aking bigger boxes than that...
=A0
How are you relaxing the system enough to do MD?
=A0
=A0
If you prefer to reply in person, e-mail is kelly.theel|-|email.ucr.edu
=A0
Thanks for any help you can give!

--
- Kelly

"Most folks are about as happy as they = make up their minds to be." =A0- Abraham Lincoln
--000e0cd10622abe6970484d735de-- From owner-chemistry@ccl.net Thu Apr 22 18:44:00 2010 From: "Jamin Krinsky jamink/a\berkeley.edu" To: CCL Subject: CCL:G: PES scan on excited state - G09 Message-Id: <-41697-100422184041-24211-z8DuPTgYSx8DhEYWAqaO/g]-[server.ccl.net> X-Original-From: Jamin Krinsky Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 22 Apr 2010 15:40:30 -0700 MIME-Version: 1.0 Sent to CCL by: Jamin Krinsky [jamink#,#berkeley.edu] Dear Jason, It may be that the scan keyword doesn't work with CIS. Try setting up the scan using the modredundant functionality instead. For instance, I just ran a dihedral scan using the following input on ethene and it gave the correct excited state minimum at 90 degrees. #p opt=3Dmodredundant cis=3D(root=3D1)/6-31g(d) nosymm Title Card Required 0 1 C -0.23037541 0.56313992 0.00000000 H 0.30278833 -0.36456500 0.00000000 H -1.30037541 0.56313992 0.00000000 C 0.44489890 1.73811722 0.00000000 H -0.08826485 2.66582214 0.00000000 H 1.51489890 1.73811722 0.00000000 D 2 1 4 6 S 5 20.000000 This specifies a dihedral between atoms 2, 1, 4 and 6, S=3Dscan, and I did 5 steps of 20.0000 degrees. Hope this helps. Jamin On Thu, Apr 22, 2010 at 11:34 AM, Jason D Biggs jbiggs2%a%uoregon.edu wrote: > > Sent to CCL by: "Jason D Biggs" [jbiggs2|,|uoregon.edu] > I am trying to get PESs for both the ground electronic state, and first e= xcited states as a function of some internal coordinate. =A0It is pretty si= mple to get the ground state curve using the "scan" keyword. =A0I can chang= e the basis set used to do the scan, and even choose between HF or DFT or M= P2. =A0But when I set the method to CIS(root=3D1) instead of HF (which, unl= ess I am mistaken, is all I need to do for an opt or freq job to get inform= ation on the S1 state instead of the ground state), I don't get a different= PES at all. =A0It seems that Gaussian instead finds all the excited states= first, then does the scan for the ground state. > > Is there any way to get Gaussian to do the scan for the first excited sin= glet state? =A0It seems like a pretty common calculation type - I often see= Born-Oppenheimer surfaces for multiple electronic states. > > If this isn't possible, I could imagine doing it myself by making a serie= s of Gaussian input files that simply found the energy of the first excited= state for a given molecular geometry - but the method I'd use to do this p= robably wouldn't be the most efficient way. > > Thanks in advance > Jason Biggs > University of Oregon > > > > -=3D This is automatically added to each message by the mailing script = =3D-> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml> =A0 =A0 =A0http://www.ccl.net/spammers.txt> > > --=20 Jamin L Krinsky, Ph.D. Molecular Graphics and Computation Facility 175 Tan Hall, University of California, Berkeley, CA 94720 jamink#,#berkeley.edu, 510-643-0616 http://glab.cchem.berkeley.edu From owner-chemistry@ccl.net Thu Apr 22 19:18:00 2010 From: "alfredo tlahuice tlahuicef]|[yahoo.com" To: CCL Subject: CCL:G: Question regarding geometry optimization Message-Id: <-41698-100422181359-6124-kuOn/jYh9qd8O0coJBtaaA===server.ccl.net> X-Original-From: alfredo tlahuice Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=iso-8859-1 Date: Thu, 22 Apr 2010 14:13:48 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: alfredo tlahuice [tlahuicef*|*yahoo.com] Hello there=0AYou need to check your atomic positions out.=0AMaybe you have= two o more atoms with the same coordinates.=0A=0ATake care.=0AAlfredo Tlah= uice=0A=0A--- On Thu, 4/22/10, Ashish D ashish.ashrock-.-gmail.com wrote:=0A=0A> From: Ashish D ashish.ashrock-.-gmail.com <= owner-chemistry-*-ccl.net>=0A> Subject: CCL:G: Question regarding geometry op= timization=0A> To: "Tlahuice, Alfredo " =0A> D= ate: Thursday, April 22, 2010, 6:12 PM=0A> =0A> Sent to CCL by: "Ashish=A0 = D" [ashish.ashrock ~~=0A> gmail.com]=0A> Hello All=0A> =0A> I am getting th= e error message in my geometry optimization.=0A> The optimization is carrie= d out at HF/6-31+G(d,p) of a T12=0A> cluster of zeolite Y.=0A> =0A> I am ge= tting the following error message :=0A> =0A> Small interatomic distances en= countered:=0A> =A0 =A0=A0=A02=A0 =A0 1=0A> =0A> =A0 =A0=A0=A03=A0 =A0 1=0A>= =0A> =A0 =A0=A0=A03=A0 =A0 2=0A> =0A> =A0 =A0=A0=A04=A0 =A0 1=0A> =0A> =A0= =A0=A0=A04=A0 =A0 2=0A> =0A> =A0 =A0=A0=A04=A0 =A0 3=0A> =0A> =A0 =A0=A0= =A05=A0 =A0 1=0A> =0A> =A0 =A0=A0=A05=A0 =A0 2=0A> =0A> =A0 =A0=A0=A05=A0 = =A0 3=0A> =0A> =A0 =A0=A0=A05=A0 =A0 4=0A> =0A> =A0 =A0=A0=A06=A0 =A0 1=0A>= =0A> =A0 =A0=A0=A06=A0 =A0 2=0A> =0A> =A0 =A0=A0=A06=A0 =A0 3=0A> =0A> =A0= =A0=A0=A06=A0 =A0 4=0A> =0A> =A0 =A0=A0=A06=A0 =A0 5=0A> =0A> =A0 =A0=A0= =A07=A0 =A0 1=0A> =0A> =A0 =A0=A0=A07=A0 =A0 2=0A> =0A> =A0 =A0=A0=A07=A0 = =A0 3=0A> =0A> =A0 =A0=A0=A07=A0 =A0 4=0A> =0A> =A0 =A0=A0=A07=A0 =A0 5=0A>= Problem with the distance matrix.=0A> Error termination via Lnk1e in /us= r/local/g03/l202.exe=0A> =0A> =0A> Any help and suggestions will be appreci= ated.=0A> =0A> Thanks,=0A> A=0A> =0A> =0A> =0A> -=3D This is automatically = added to each message by the=0A> mailing script =3D-=0A> To recover the ema= il address of the author of the message,=0A> please change=0A> the strange = characters on the top line to the -*- sign. You=0A> can also=0A> look up the = X-Original-From: line in the mail header.=0A> =0A> E-mail to subscribers: C= HEMISTRY-*-ccl.net=0A> or use:=0A> =A0 =A0 =A0 http://www.ccl.net/cgi-bin/ccl= /send_ccl_message=0A> =0A> E-mail to administrators: CHEMISTRY-REQUEST-*-ccl.= net=0A> or use=0A> =A0 =A0 =A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_mess= age=0A> =0A=0A> =A0 =A0 =A0 http://www.ccl.net/che= mistry/sub_unsub.shtml=0A> =0A> Before posting, check wait time at: http://= www.ccl.net=0A> =0A=0A> Conferences: http://= server.ccl.net/chemistry/announcements/conferences/=0A> =0A> Search Message= s: http://www.ccl.net/chemistry/searchccl/index.shtml=0A> =0A> If your mail= bounces from CCL with 5.7.1 error, check:=0A> =A0 =A0 =A0 http://www.ccl.n= et/spammers.txt=0A> =0A> RTFI: http://www.ccl.net/chemistry/aboutccl/instru= ctions/=0A> =0A> =0A> =0A=0A=0A From owner-chemistry@ccl.net Thu Apr 22 20:36:00 2010 From: "Eric Scerri scerri{=}chem.ucla.edu" To: CCL Subject: CCL: latest issue FOCH/ Special issue on the Periodic Table Message-Id: <-41699-100422154259-27177-Ar+5wkegaBH8qwMO+FLgoA__server.ccl.net> X-Original-From: Eric Scerri Content-Type: multipart/alternative; boundary=Apple-Mail-22--549679627 Date: Thu, 22 Apr 2010 11:59:40 -0700 Mime-Version: 1.0 (Apple Message framework v753.1) Sent to CCL by: Eric Scerri [scerri__chem.ucla.edu] --Apple-Mail-22--549679627 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > > Foundations of Chemistry > http://www.springerlink.com/content/rj140x68v1w2/? > p=fb1d0ac44f0243da8138d2831c133846&pi=0 > Volume 12, Number 1 / April, 2010 > > Special Issue on the Periodic Table > > > > > Editorial 34 > Eric R. Scerri > > > > Article > Charles Janet: unrecognized genius of the periodic system > Philip J. Stewart > > > Article > The group VIII platinum-group metals and the Periodic Table > W. P. Griffith > > > Article > The question mark at uranium > M. J. Laing > > > Article > Metals: typical and less typical, transition and inner transition > Fathi Habashi > > > Article > Explaining the periodic table, and the role of chemical triads > Eric Scerri > > > > Article > Newlands revisited: a display of the periodicity of the chemical > elements for chemists > E. G. Marks and J. A. Marks > L > > > > > > Eric Scerri, The Periodic Table, Its Story and Its Significance, > Oxford University Press, 2007 > http://www.oup.com/us/catalog/general/subject/Chemistry/? > view=usa&ci=9780195305739 > > > > > ------------------------------------------------------------------------ ----------------------------------------------------------------------- The Periodic Table: Its Story and Its Significance, by Eric Scerri, Oxford University Press, 2007. named as "Outstanding Academic Book for 2007" by Choice Library Magazine. Collected Papers on Philosophy of Chemistry, Imperial College Press, 2008. Selected Papers on the Periodic Table by Eric Scerri, Imperial College Press, 2009. --Apple-Mail-22--549679627 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=US-ASCII

   

Foundations of = Chemistry
http://www.springerlink.com/content/rj140= x68v1w2/?p=3Dfb1d0ac44f0243da8138d2831c133846&pi=3D0=

Volume 12, Number 1 / April, 2010

Special Issue on the Periodic = Table

=



= Editorial 34
Eric= R. Scerri
3D"Open

=

Article
Charles Janet: unrecognized genius = of the periodic system
= P= hilip J. Stewart

 3D"Full =
= Article
The group VIII platinum-group = metals and the Periodic Table
= W. = P. Griffith

 3D"Full =
= Article
The question mark at uranium =
M. J. = Laing

=

Article
Metals: typical and less typical, = transition and inner transition
= Fathi= Habashi
 

Article
Explaining the periodic table, and = the role of chemical triads
= Eric = Scerri
=
3D"Full
=

     
=
Article =
Newlands revisited: a display of = the periodicity of the chemical elements for chemists =
E. G. = Marks and J. A. = Marks
=
3D"FullL3D"Open 





=
Eric Scerri, The Periodic = Table, Its Story and Its Significance, Oxford University Press, = 2007
=



The Periodic = Table: Its Story and Its Significance, by Eric Scerri, Oxford University = Press, 2007.
named as "Outstanding Academic = Book for 2007" by Choice Library = Magazine.

Collected Papers = on Philosophy of Chemistry, Imperial College Press, = 2008.

Selected Papers on the Periodic Table by = Eric Scerri, Imperial College Press, = 2009.


= --Apple-Mail-22--549679627--