From owner-chemistry@ccl.net Tue May 17 10:27:01 2016 From: "Jim Kress jimkress35%gmail.com" To: CCL Subject: CCL:G: Not able to optimize structure - bisphosphole Message-Id: <-52210-160517101249-10078-fbfeIsi1HPKxeZQbe2227Q,,server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Type: multipart/alternative; boundary="----=_NextPart_000_0691_01D1B024.A1F4EEF0" Date: Tue, 17 May 2016 10:12:34 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [jimkress35__gmail.com] This is a multipart message in MIME format. ------=_NextPart_000_0691_01D1B024.A1F4EEF0 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Also, you should consider eliminating the diffuse functions from your = basis set and make sure you are using the pure 5D and 7F basis = specifications. With all the diffuse functions in your current = calculation, you most certainly have significant linear dependence of = your atomic basis functions which will result in no or poor SCF = convergence. =20 Jim =20 > From: owner-chemistry+jimkress35=3D=3Dgmail.com/a\ccl.net = [mailto:owner-chemistry+jimkress35=3D=3Dgmail.com/a\ccl.net] On Behalf Of = Daniel Morales Salazar danielmoralessalazar91- -gmail.com Sent: Monday, May 16, 2016 4:37 PM To: Kress, Jim Subject: CCL:G: Not able to optimize structure - bisphosphole =20 I am sorry, I sent the -email while editing. Hello everybody, Thanks a lot for the replies. Dear Dr. Layec, I just realized that the only try that passed had the = following input: # opt=3D(calcfc, loose, cartesian) pm6 nosymm scf=3Dqc Dear Dr. Molt, I am not sure if I understood your question correctly, = but I believe tungsten is a singlet in these cases, the spin question, I = am not sure but, should it be zero? I am not sure how to answer this = question right about now (need to read my organometallics textbook! :)) By the way I forgot to mention on the original post that I am trying DFT = methods as well but since they are taking so long to finish I started = the semi-empirical calculations thinking they would be straight forward = (oh was I wrong). For the DFT I am using a combination of basis sets = combined with pseudo-core potentials for the tungsten C H O P S 0 6-311G** **** W 0 MWB **** =20 W 0 ECP60MWB 5 60 Ultimately, it did not pass on time so I will restart from the last = geometry soon. There were a couple of PM6 that did not finish on time on the = interactive session so I do not know if I should restart them now that = you said it was ambitious. I also thought about making the calculation with smaller atoms such as = chromium and maybe changing the phenyl ligands for methyl groups, but = being a "dimeric" structure, I do not want to obtain something = completely different using smaller ligands. Dear Dr. Shobe, With the Amber it crashed immediately, but with the UFF it did go = through some steps. When I search for Energy in the output I find: " Convergence criteria 0.00011250 0.00007500 0.00045000 = 0.00030000 Step NS ND Rises OKQ Scale Max. Force RMS Force Max. Disp. RMS = Disp. Energy Flag .....bunch of steps 2093 0 0 F T 1.61D+00 0.00009841 0.00001833 0.00009354 = 0.00002815 0.3068418 =3D=3D=3D=3D Energy=3D 0.306841771" Then, " Item Value Threshold Converged? Maximum Force 0.000097 0.000450 YES RMS Force 0.000018 0.000300 YES Maximum Displacement 0.110212 0.001800 NO RMS Displacement 0.014639 0.001200 NO Predicted change in Energy=3D-1.662896D-05" Then, "Convergence limit is 0.750E-04 MaxStp=3D 10000 StMxLn=3D 3.00D-04 = StpMin=3D 1.00D-06. Convergence criteria 0.00011250 0.00007500 0.00045000 = 0.00030000 Step NS ND Rises OKQ Scale Max. Force RMS Force Max. Disp. RMS = Disp. Energy Flag 1 0 0 F T 1.00D+00 0.00017298 0.00001595 0.00017298 = 0.00001595 0.3068252 -+++ 2 0 0 F T 1.47D+00 0.00007243 0.00000955 0.00013885 = 0.00001595 0.3068252 =3D=3D=3D=3D Energy=3D 0.306825172 " Finally, " Item Value Threshold Converged? Maximum Force 0.000070 0.000450 YES RMS Force 0.000010 0.000300 YES Maximum Displacement NaN 0.001800 YES RMS Displacement NaN 0.001200 YES Predicted change in Energy=3D NaN" For the other UFF trial, there were more results for the Energy word, so = I guess it went slightly better, I will just paste shorter versions = starting from the top of the output: "Step NS ND Rises OKQ Scale Max. Force RMS Force Max. Disp. RMS = Disp. Energy Flag 1 0 0 F T 1.00D+00 0.00000000 0.00000000 0.00000000 = 0.00000000 0.8772618 =3D=3D=3D=3D Energy=3D 0.877261757 NIter=3D 0." " Energy=3D 0.849329056" " Energy=3D 0.813651610" " Energy=3D 0.771900194" "Energy=3D 0.724817194 " ..... " Energy=3D 0.623211212" " Energy=3D 0.612600532" Item Value Threshold Converged? Maximum Force 0.037731 0.000450 NO RMS Force 0.005556 0.000300 NO Maximum Displacement 0.051140 0.001800 NO RMS Displacement 0.007356 0.001200 NO Predicted change in Energy=3D-1.136353D-02 Optimization stopped. -- Number of steps exceeded, NStep=3D 10 =20 =20 I do not have an atom type or anything for tungsten, the input of the = UFF looks like: # opt=3Dcalcfc uff geom=3Dconnectivity =20 I used the ones available in Gaussian 09 , UFF, as I said before.=20 It has 60 atoms, I realized the typo, and I was waiting for someone to = notice thanks. Yes, for the later jobs I am, but those did not finish on time during = the interactive session.=20 Unfortunately I am way past my allocated hours per month so I get very = low priorities in my jobs now. =20 Guess=3DRead does seem to be working with the later jobs, and I do = believe the tungsten is in the correct electronic state.=20 Just a friendly reminder that before Gaussian, I preoptimized the = structures first in chem3d using MM2 then in Avogadro using UFF. So I = was pretty surprised to see that Gaussian failed. Thank you everybody for the replies. I hope my DFT on queue will pass = this time. Sincerely, Daniel Morales Salazar Bachelor of Science in Chemistry, Georgia Institute of Technology PhD student, Department of Chemistry - =C3=85ngstr=C3=B6m Laboratory=20 Uppsala University=20 Box 523 SE-751 20 Uppsala Sweden =20 On Mon, May 16, 2016 at 10:15 PM, Daniel Morales Salazar = > wrote: Hello everybody, Thanks a lot for the replies. Dear Dr. Layec, I just realized that the only try that passed had the = following input: # opt=3D(calcfc, loose, cartesian) pm6 nosymm scf=3Dqc Dear Dr. Molt, I am not sure if I understood your question correctly, = but I believe tungsten is a singlet in these cases, the spin question, I = am not sure but, should it be zero? I am not sure how to answer this = question right about now (need to read my organometallics textbook! :)) By the way I forgot to mention on the original post that I am trying DFT = methods as well but since they are taking so long to finish I started = the semi-empirical calculations thinking they would be straight forward = (oh was I wrong). For the DFT I am using a combination of basis sets = combined with pseudo-core potentials for the tungsten C H O P S 0 6-311G** **** W 0 MWB **** =20 W 0 ECP60MWB 5 60 Ultimately, it did not pass on time so I will restart from the last = geometry soon. There were a couple of PM6 I also thought about making the calculation with smaller atoms such as = chromium and maybe changing the phenyl ligands for methyl groups, but = being a "dimeric" structure, I do not want to obtain something = completely different using smaller ligands. Dear Dr. Shobe, With the Amber it crashed immediately, I am assuming tungsten was not = parametr Daniel-- A few questions, that may be useful to others even if not to me :-) First regarding the MM methods. The error message given is pretty = generic. Does the calculation produce any intermediate geometries, or = does it crash on the first geometric-optimization step? If there are = intermediate geometries,does the energy decrease from step to step, or = is there a sudden increase in energy? Do you even have an atom type and = parameters for tungsten? Which MM force field are you using? [I would have advised opt=3Dcalcall as a last resort, but given the size = of your molecule (which is surely even bigger than the formula you = actually wrote implies: how many carbon atoms again? :-) I might have = second thoughts on that. Hopefully someone has a better idea.] About the semiemprical method (PM6). It appears from the error message = that you are not getting a decent wavefunction. Are you using = guess=3Dread to get the wavefunction from the checkpoint file in which = you were able to optimize with opt=3Dloose? (Or does guess=3Dread even = work with semiempirical methods?) Are you sure everything (especially = the tungsten moieties) are in the correct electronic state?=20 Hope this helps,--David Shobe =20 SCF Energy R -1.229246327147848E+00 Total Energy R -1.229246327147848E+00 RMS Force R 2.869324126432187E-04 =20 =20 On Sat, May 14, 2016 at 10:42 PM, David Shobe avidshobe-$-yahoo.com = > wrote: Daniel-- A few questions, that may be useful to others even if not to me :-) First regarding the MM methods. The error message given is pretty = generic. Does the calculation produce any intermediate geometries, or = does it crash on the first geometric-optimization step? If there are = intermediate geometries,does the energy decrease from step to step, or = is there a sudden increase in energy? Do you even have an atom type and = parameters for tungsten? Which MM force field are you using? [I would have advised opt=3Dcalcall as a last resort, but given the size = of your molecule (which is surely even bigger than the formula you = actually wrote implies: how many carbon atoms again? :-) I might have = second thoughts on that. Hopefully someone has a better idea.] About the semiemprical method (PM6). It appears from the error message = that you are not getting a decent wavefunction. Are you using = guess=3Dread to get the wavefunction from the checkpoint file in which = you were able to optimize with opt=3Dloose? (Or does guess=3Dread even = work with semiempirical methods?) Are you sure everything (especially = the tungsten moieties) are in the correct electronic state?=20 Hope this helps,--David Shobe On Saturday, May 14, 2016 9:10 AM, Daniel Morales Salazar = danielmoralessalazar91]_[gmail.com = > wrote: Sent to CCL by: "Daniel Morales Salazar" = [danielmoralessalazar91*|*gmail.com ] Hello, I am trying to optimize a molecule with the chemical formula = CH52O18P4S4W2, which contains thiophenes-phospholes, phenyl groups, and tungsten pentacarbonyl substituents. It is a large and especially bulky molecule. I have tried using MM and Semi-empirical methods (PM6) unsuccessfully. The only converged trial so far was one with the "loose" keyword using PM6, which crashed in the following calculation with stricter parameters when I did not use the keyword. I have tried the keywords calcfc, qc, cartesian, etc. Any advice for these types of cases? Semi-empirical jobs crash with the message: "Symmetry turned off by external request. DSYEV returned Info=3D 2 IAlg=3D 2 N=3D 3 NDim=3D 3 = NE2=3D =20 2. Diagonalization in DiagDN failed." MM methods crash with the message: " Error termination request processed by link 9999." I have the feeling that the initial geometries are not so bad even! = Thank you very much for your help. Sincerely, Daniel Morales Salazar -=3D This is automatically added to each message by the mailing script = =3D-= ------_Part_2073303_152685841.1463258551881 Content-Type: text/html; charsetUTF-8 Content-Transfer-Encoding: quoted-printable
Daniel--
<= div = id=3D"yiv3733130765yui_3_16_0_ym19_1_1463251158989_22609">
A few = questions, that may be useful to others even if not to me :-)

First = regarding the MM methods.  The error message given is pretty = generic.  Does the calculation produce any intermediate geometries, = or does it crash on the first geometric-optimization step?  If = there are intermediate geometries,does the energy decrease from step to = step, or is there a sudden increase in energy?  Do you even have an = atom type and parameters for tungsten?  Which MM force field are = you using?

[I = would have advised opt=3Dcalcall as a last resort, but given the size of = your molecule (which is surely even bigger than the formula you actually = wrote implies: how many carbon atoms again? :-) I might have second = thoughts on that.  Hopefully someone has a better idea.]

About the semiemprical method (PM6).  It appears from = the error message that you are not getting a decent wavefunction. =  Are you using guess=3Dread to get the wavefunction from the = checkpoint file in which you were able to optimize with opt=3Dloose? =  (Or does guess=3Dread even work with semiempirical methods?) =  Are you sure everything (especially the tungsten moieties) are in = the correct electronic state? 

Hope this helps,
--David Shobe








On Saturday, May 14, 2016 = 9:10 AM, Daniel Morales Salazar danielmoralessalazar91]_[gmail.com = <owner-chemistry++ccl.net > = wrote:



Sent to CCL by: "Daniel  Morales Salazar" = [danielmoralessalazar91*|*gmail.com ]
Hello,

I am trying = to optimize a molecule with the chemical formula CH52O18P4S4W2, which = contains thiophenes-phospholes, phenyl groups, and
tungsten pentacarbonyl substituents.

It is a large and especially bulky = molecule. I have tried using MM and
Semi-empirical = methods (PM6) unsuccessfully. The only converged trial so
far was one with the "loose" keyword using PM6, which = crashed in the
following calculation with stricter = parameters when I did not use the
keyword. I have = tried the keywords calcfc, qc, cartesian, etc.

Any advice for these types of cases?

Semi-empirical jobs crash with the = message:

"Symmetry turned off by = external request.
DSYEV returned Info=3D    =       2 IAlg=3D 2 N=3D    3 NDim=3D  =   3 NE2=3D         
2.
Diagonalization in DiagDN = failed."

MM methods crash with the = message:

" Error termination = request processed by link 9999."

I = have the feeling that the initial geometries are not so bad even! Thank =
you very much for your help.

Sincerely,

Daniel = Morales Salazar



-=3D This is automatically added to = each message by the mailing script =3D-
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=
=20 --=20 Daniel Morales Salazar Bachelor of Science in Chemistry, Georgia Institute of Technology PhD student, Department of Chemistry - =C3=85ngstr=C3=B6m Laboratory=20 Uppsala University=20 Box 523 SE-751 20 Uppsala Sweden =20 =20 =20 --=20 Daniel Morales Salazar Bachelor of Science in Chemistry, Georgia Institute of Technology PhD student, Department of Chemistry - =C3=85ngstr=C3=B6m Laboratory=20 Uppsala University=20 Box 523 SE-751 20 Uppsala Sweden =20 =20 ------=_NextPart_000_0691_01D1B024.A1F4EEF0 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable

Also, you should consider eliminating the diffuse functions from your = basis set and make sure you are using the pure 5D and 7F basis = specifications.=C2=A0 With all the diffuse functions in your current = calculation, you most certainly have significant linear dependence of = your atomic basis functions which will result in no or poor SCF = convergence.

 

Jim

 

From:<= /b> = owner-chemistry+jimkress35=3D=3Dgmail.com/a\ccl.net = [mailto:owner-chemistry+jimkress35=3D=3Dgmail.com/a\ccl.net] On Behalf = Of Daniel Morales Salazar danielmoralessalazar91- = -gmail.com
Sent: Monday, May 16, 2016 4:37 PM
To: = Kress, Jim <jimkress35/a\gmail.com>
Subject: = CCL:G: Not able to optimize structure - = bisphosphole

 

I am = sorry, I sent the -email while editing.
Hello everybody,

Thanks a lot for the = replies.

Dear Dr. Layec, I just realized that the only try = that passed had the following input:

# opt=3D(calcfc, loose, = cartesian) pm6 nosymm scf=3Dqc


Dear Dr. Molt, I am not = sure if I understood your question correctly, but I believe tungsten is = a singlet in these cases, the spin question, I am not sure but, should = it be zero? I am not sure how to answer this question right about now = (need to read my organometallics textbook! :))
By the way I forgot to = mention on the original post that I am trying DFT methods as well but = since they are taking so long to finish I started the semi-empirical = calculations thinking they would be straight forward (oh was I wrong). = For the DFT I am using a combination of basis sets combined with = pseudo-core potentials for the tungsten

C H O P S = 0

6-311G**

****

W = 0

MWB

****

 

W = 0

ECP60MWB = 5 60

Ultimately, it did = not pass on time so I will restart from the last geometry = soon.

There were a couple = of PM6 that did not finish on time on the interactive session so I do = not know if I should restart them now that you said it was = ambitious.

I also thought = about making the calculation with smaller atoms such as chromium and = maybe changing the phenyl ligands for methyl groups, but being a = "dimeric" structure, I do not want to obtain something = completely different using smaller ligands.

Dear Dr. = Shobe,
With the Amber it = crashed immediately, but with the UFF it did go through some steps. When = I search for Energy in the output I find:

" Convergence = criteria             0.00011250 0.00007500 = 0.00045000 0.00030000

  Step  NS =  ND Rises OKQ   Scale  Max. Force  RMS Force Max. = Disp.  RMS Disp.     Energy   = Flag

.....bunch of = steps

 2093   0   0   F   =  T  1.61D+00 0.00009841 0.00001833 0.00009354 0.00002815 =    0.3068418 =3D=3D=3D=3D

 Energy=3D   =  0.306841771"
Then,
" Item     =           Value     Threshold =  Converged?

 Maximum Force =            0.000097     0.000450 =     YES

 RMS   =   Force            0.000018   =   0.000300     YES

 Maximum = Displacement     0.110212     0.001800     = NO

 RMS     Displacement   =   0.014639     0.001200     = NO

 Predicted change in = Energy=3D-1.662896D-05"
Then,
 "Convergence limit = is  0.750E-04 MaxStp=3D 10000 StMxLn=3D 3.00D-04 StpMin=3D = 1.00D-06.

 Convergence criteria     =         0.00011250 0.00007500 0.00045000 = 0.00030000

  Step  NS  ND Rises OKQ   = Scale  Max. Force  RMS Force Max. Disp.  RMS Disp.   =   Energy   Flag

     1 =   0   0   F    T  1.00D+00 0.00017298 = 0.00001595 0.00017298 0.00001595    0.3068252 = -+++

     2   0   0   = F    T  1.47D+00 0.00007243 0.00000955 0.00013885 = 0.00001595    0.3068252 = =3D=3D=3D=3D

 Energy=3D    0.306825172 =  "

Finally,

 " Item =               Value     = Threshold  Converged?

 Maximum Force =            0.000070     0.000450 =     YES

 RMS   =   Force            0.000010   =   0.000300     YES

 Maximum = Displacement          NaN     = 0.001800     YES

 RMS   =   Displacement          NaN     = 0.001200     YES

 Predicted change = in Energy=3D         =  NaN"

For the = other UFF trial, there were more results for the Energy word, so I guess = it went slightly better, I will just paste shorter versions starting = > from the top of the output:

"Step  NS =  ND Rises OKQ   Scale  Max. Force  RMS Force Max. = Disp.  RMS Disp.     Energy   = Flag

     1   0   0   = F    T  1.00D+00 0.00000000 0.00000000 0.00000000 = 0.00000000    0.8772618 = =3D=3D=3D=3D

 Energy=3D    0.877261757 =     NIter=3D   0."
" Energy=3D   =  0.849329056"
" Energy=3D   =  0.813651610"
" Energy=3D   =  0.771900194"

"Energy=3D   =  0.724817194 "
.....
" Energy=3D   =  0.623211212"
" Energy=3D   =  0.612600532"

 Item   =             Value     Threshold =  Converged?

 Maximum Force =            0.037731     0.000450 =     NO

 RMS   =   Force            0.005556   =   0.000300     NO

 Maximum = Displacement     0.051140     0.001800     = NO

 RMS     Displacement   =   0.007356     0.001200     = NO

 Predicted change in = Energy=3D-1.136353D-02

 Optimization = stopped.

    -- Number of steps exceeded, =  NStep=3D  10

 

 

I do not have an atom = type or anything for tungsten, the input of the UFF looks = like:

# opt=3Dcalcfc uff = geom=3Dconnectivity

 

I used the ones = available in Gaussian 09 , UFF, as I said before.

It has 60 = atoms, I realized the typo, and I was waiting for someone to notice = thanks.

Yes, for the later jobs I am, but those did not finish on = time during the interactive session.

Unfortunately I am way past = my allocated hours per month so I get very low priorities in my jobs = now.
 
Guess=3DRead does seem to be working with the later = jobs, and I do believe the tungsten is in the correct electronic = state. 

Just a friendly reminder that before Gaussian, I = preoptimized the structures first in chem3d using MM2 then in Avogadro = using UFF. So I was pretty surprised to see that Gaussian = failed.

Thank you everybody for the replies. I hope my DFT on = queue will pass this time.

Sincerely,

Daniel Morales = Salazar

Bachelor of = Science in Chemistry, Georgia Institute of Technology

PhD = student, Department of Chemistry - =C3=85ngstr=C3=B6m Laboratory =

Uppsala = University

Box = 523

SE-751 20 = Uppsala

Sweden<= /o:p>

 

On Mon, = May 16, 2016 at 10:15 PM, Daniel Morales Salazar <danielmoralessalazar91%gmail.com> = wrote:

Hello everybody,

Thanks a lot for the = replies.

Dear Dr. Layec, I just realized that the only try = that passed had the following input:

# opt=3D(calcfc, loose, = cartesian) pm6 nosymm scf=3Dqc


Dear Dr. Molt, I am not = sure if I understood your question correctly, but I believe tungsten is = a singlet in these cases, the spin question, I am not sure but, should = it be zero? I am not sure how to answer this question right about now = (need to read my organometallics textbook! :))
By the way I forgot to = mention on the original post that I am trying DFT methods as well but = since they are taking so long to finish I started the semi-empirical = calculations thinking they would be straight forward (oh was I wrong). = For the DFT I am using a combination of basis sets combined with = pseudo-core potentials for the tungsten

C H O P S 0

6-311G**

****

W = 0

MWB

****

 

W = 0

ECP60MWB 5 60

Ultimately, it did = not pass on time so I will restart from the last geometry = soon.

There were a couple of PM6

I also thought about = making the calculation with smaller atoms such as chromium and maybe = changing the phenyl ligands for methyl groups, but being a = "dimeric" structure, I do not want to obtain something = completely different using smaller ligands.

Dear Dr. Shobe,
With the Amber it crashed = immediately, I am assuming tungsten was not = parametr


Daniel--

A few questions, that may be useful to others even if = not to me :-)

First = regarding the MM methods.  The error message given is pretty = generic.  Does the calculation produce any intermediate geometries, = or does it crash on the first geometric-optimization step?  If = there are intermediate geometries,does the energy decrease from step to = step, or is there a sudden increase in energy?  Do you even have an = atom type and parameters for tungsten?  Which MM force field are = you using?

[I would have = advised opt=3Dcalcall as a last resort, but given the size of your = molecule (which is surely even bigger than the formula you actually = wrote implies: how many carbon atoms again? :-) I might have second = thoughts on that.  Hopefully someone has a better = idea.]

About the = semiemprical method (PM6).  It appears from the error message that = you are not getting a decent wavefunction.  Are you using = guess=3Dread to get the wavefunction from the checkpoint file in which = you were able to optimize with opt=3Dloose?  (Or does guess=3Dread = even work with semiempirical methods?)  Are you sure everything = (especially the tungsten moieties) are in the correct electronic = state? 

Hope this = helps,--David Shobe

 

SCF = Energy                   =               R     = -1.229246327147848E+00

Total Energy             =                   R   =   -1.229246327147848E+00

RMS Force             =                     =  R     =  2.869324126432187E-04

 



 

On Sat, May 14, 2016 at 10:42 PM, David Shobe = avidshobe-$-yahoo.com = <owner-chemistry%ccl.net> = wrote:

Daniel--
A few questions, that may be useful to = others even if not to me :-)
First regarding the MM methods.  = The error message given is pretty generic.  Does the calculation = produce any intermediate geometries, or does it crash on the first = geometric-optimization step?  If there are intermediate = geometries,does the energy decrease from step to step, or is there a = sudden increase in energy?  Do you even have an atom type and = parameters for tungsten?  Which MM force field are you using?
[I = would have advised opt=3Dcalcall as a last resort, but given the size of = your molecule (which is surely even bigger than the formula you actually = wrote implies: how many carbon atoms again? :-) I might have second = thoughts on that.  Hopefully someone has a better idea.]
About = the semiemprical method (PM6).  It appears from the error message = that you are not getting a decent wavefunction.  Are you using = guess=3Dread to get the wavefunction from the checkpoint file in which = you were able to optimize with opt=3Dloose?  (Or does guess=3Dread = even work with semiempirical methods?)  Are you sure everything = (especially the tungsten moieties) are in the correct electronic = state? 
Hope this helps,--David = Shobe







 On Saturday, May 14, 2016 = 9:10 AM, Daniel Morales Salazar danielmoralessalazar91]_[gmail.com = <owner-chemistry++ccl.net> wrote:



Sent to CCL by: = "Daniel  Morales Salazar" [danielmoralessalazar91*|*gmail.com]
Hello,

I am trying to = optimize a molecule with the chemical formula CH52O18P4S4W2, which = contains thiophenes-phospholes, phenyl groups, and
tungsten = pentacarbonyl substituents.

It is a large and especially bulky = molecule. I have tried using MM and
Semi-empirical methods (PM6) = unsuccessfully. The only converged trial so
far was one with the = "loose" keyword using PM6, which crashed in the
following = calculation with stricter parameters when I did not use the
keyword. = I have tried the keywords calcfc, qc, cartesian, etc.

Any advice = for these types of cases?

Semi-empirical jobs crash with the = message:

"Symmetry turned off by external = request.
 DSYEV returned Info=3D        =   2 IAlg=3D 2 N=3D    3 NDim=3D    3 = NE2=3D         
2.
 Diagonalization = in DiagDN failed."

MM methods crash with the = message:

" Error termination request processed by link = 9999."

I have the feeling that the initial geometries are = not so bad even! Thank
you very much for your = help.

Sincerely,

Daniel Morales = Salazar



-=3D This is automatically added to each message = by the mailing script =3D-         =  Subscribe/Unsubscribe:
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<html><head></head><body>= <div style=3D"color:#000; background-color:#fff; = font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida = Grande, sans-serif;font-size:13px"><div = id=3D"yiv3733130765"><div = id=3D"yui_3_16_0_ym19_1_1463251158989_27956"><div = style=3D"color:#000;background-color:#fff;font-family:HelveticaNeue,= Helvetica Neue, Helvetica, Arial, Lucida Grande, = sans-serif;font-size:13px;" = id=3D"yui_3_16_0_ym19_1_1463251158989_27955"><div = id=3D"yiv3733130765yui_3_16_0_ym19_1_1463251158989_22609">Da= niel--</div><div = id=3D"yiv3733130765yui_3_16_0_ym19_1_1463251158989_22609">&l= t;br></div><div = id=3D"yiv3733130765yui_3_16_0_ym19_1_1463251158989_22609">A = few questions, that may be useful to others even if not to me = :-)</div><div = id=3D"yiv3733130765yui_3_16_0_ym19_1_1463251158989_22609">&l= t;br></div><div = id=3D"yiv3733130765yui_3_16_0_ym19_1_1463251158989_22609">Fi= rst regarding the MM methods. &nbsp;The error message given is = pretty generic. &nbsp;Does the calculation produce any intermediate = geometries, or does it crash on the first geometric-optimization step? = &nbsp;If there are intermediate geometries,does the energy decrease = > from step to step, or is there a sudden increase in energy? &nbsp;Do = you even have an atom type and parameters for tungsten? &nbsp;Which = MM force field are you using?</div><div = id=3D"yiv3733130765yui_3_16_0_ym19_1_1463251158989_22609">&l= t;br></div><div = id=3D"yiv3733130765yui_3_16_0_ym19_1_1463251158989_22609" = dir=3D"ltr">[I would have advised opt=3Dcalcall as a last = resort, but given the size of your molecule (which is surely even bigger = than the formula you actually wrote implies: how many carbon atoms = again? :-) I might have second thoughts on that. &nbsp;Hopefully = someone has a better idea.]</div><div = id=3D"yiv3733130765yui_3_16_0_ym19_1_1463251158989_22609">&l= t;br clear=3D"none"></div><div = id=3D"yiv3733130765yui_3_16_0_ym19_1_1463251158989_22609" = dir=3D"ltr">About the semiemprical method (PM6). = &nbsp;It appears from the error message that you are not getting a = decent wavefunction. &nbsp;Are you using guess=3Dread to get the = wavefunction from the checkpoint file in which you were able to optimize = with opt=3Dloose? &nbsp;(Or does guess=3Dread even work with = semiempirical methods?) &nbsp;Are you sure everything (especially = the tungsten moieties) are in the correct electronic = state?&nbsp;</div><div = id=3D"yiv3733130765yui_3_16_0_ym19_1_1463251158989_22609" = dir=3D"ltr"><br></div><div = id=3D"yiv3733130765yui_3_16_0_ym19_1_1463251158989_22609" = dir=3D"ltr">Hope this helps,</div><div = id=3D"yiv3733130765yui_3_16_0_ym19_1_1463251158989_22609" = dir=3D"ltr">--David Shobe</div><div = id=3D"yiv3733130765yui_3_16_0_ym19_1_1463251158989_22609">&l= t;br clear=3D"none"></div><div = id=3D"yiv3733130765yui_3_16_0_ym19_1_1463251158989_22609">&l= t;br clear=3D"none"></div><div = id=3D"yiv3733130765yui_3_16_0_ym19_1_1463251158989_22613">&l= t;br clear=3D"none"></div><div = id=3D"yiv3733130765yui_3_16_0_ym19_1_1463251158989_23060">&l= t;br clear=3D"none"></div><div = class=3D"yiv3733130765qtdSeparateBR" = id=3D"yui_3_16_0_ym19_1_1463251158989_27957"><br = clear=3D"none"><br = clear=3D"none"></div></div></div></div&= gt;<div class=3D".yiv3733130765yahoo_quoted"> <div = style=3D"font-family:HelveticaNeue, Helvetica Neue, Helvetica, = Arial, Lucida Grande, sans-serif;font-size:13px;"> <div = style=3D"font-family:HelveticaNeue, Helvetica Neue, Helvetica, = Arial, Lucida Grande, sans-serif;font-size:16px;"> <div = class=3D"qtdSeparateBR"><br><br></div><= div class=3D"yiv3733130765yqt3542491216" = id=3D"yiv3733130765yqtfd16282"><div = dir=3D"ltr"><font size=3D"2" = face=3D"Arial"> On Saturday, May 14, 2016 9:10 AM, Daniel = Morales Salazar danielmoralessalazar91]_[gmail.com &lt;owner-chemistry++ccl.net&gt; = wrote:<br clear=3D"none"></font></div>  = <br clear=3D"none"><br clear=3D"none"> = <div class=3D"yiv3733130765y_msg_container"><br = clear=3D"none">Sent to CCL by: "Daniel&nbsp; = Morales Salazar" [danielmoralessalazar91*|*gmail.com]<br = clear=3D"none">Hello, <br = clear=3D"none"><br clear=3D"none">I am = trying to optimize a molecule with the chemical formula CH52O18P4S4W2, = which contains thiophenes-phospholes, phenyl groups, and <br = clear=3D"none">tungsten pentacarbonyl substituents.<br = clear=3D"none"><br clear=3D"none">It is a = large and especially bulky molecule. I have tried using MM and <br = clear=3D"none">Semi-empirical methods (PM6) unsuccessfully. = The only converged trial so <br clear=3D"none">far was = one with the "loose" keyword using PM6, which crashed in the = <br clear=3D"none">following calculation with stricter = parameters when I did not use the <br = clear=3D"none">keyword. I have tried the keywords calcfc, = qc, cartesian, etc. <br clear=3D"none"><br = clear=3D"none">Any advice for these types of cases?<br = clear=3D"none"><br = clear=3D"none">Semi-empirical jobs crash with the = message:<br clear=3D"none"><br = clear=3D"none">"Symmetry turned off by external = request.<br clear=3D"none"> DSYEV returned = Info=3D&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;  2 = IAlg=3D 2 N=3D&nbsp; &nbsp;  3 NDim=3D&nbsp; = &nbsp;  3 NE2=3D&nbsp; &nbsp; &nbsp; &nbsp; = &nbsp;  <br clear=3D"none">2.<br = clear=3D"none"> Diagonalization in DiagDN = failed."<br clear=3D"none"><br = clear=3D"none">MM methods crash with the message:<br = clear=3D"none"><br clear=3D"none">" = Error termination request processed by link 9999."<br = clear=3D"none"><br clear=3D"none">I have = the feeling that the initial geometries are not so bad even! Thank = <br clear=3D"none">you very much for your help.<br = clear=3D"none"><br = clear=3D"none">Sincerely,<br = clear=3D"none"><br clear=3D"none">Daniel = Morales Salazar<br clear=3D"none"><br = clear=3D"none"><br clear=3D"none"><br = clear=3D"none">-=3D This is automatically added to each = message by the mailing script =3D-<br clear=3D"none">To = recover the email address of the author of the message, please = change<br clear=3D"none">the strange characters on the = top line to the ++ sign. 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-- =

Daniel Morales = Salazar

Bachelor of Science in Chemistry, Georgia = Institute of Technology

PhD = student, Department of Chemistry - = =C3=85ngstr=C3=B6m Laboratory 

Uppsala = University 

Box = 523

SE-751 20 = Uppsala

Sweden

 

 



 

-- =

Daniel = Morales Salazar

Bachelor of = Science in Chemistry, Georgia Institute of = Technology

PhD = student, Department of Chemistry - = =C3=85ngstr=C3=B6m Laboratory 

Uppsala University 

Box 523

SE-751 20 Uppsala

Sweden

 

 

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