From owner-chemistry@ccl.net Tue Aug 22 09:02:00 2017 From: "David Shobe shobedavid]![gmail.com" To: CCL Subject: CCL:G: Wfn to wfx converter? Message-Id: <-52941-170821221807-17629-gaNt/bIrLhW/QgQiSOzzeQ()server.ccl.net> X-Original-From: David Shobe Content-Type: multipart/alternative; boundary="001a114e5fec44f33e05574e340b" Date: Mon, 21 Aug 2017 21:17:59 -0500 MIME-Version: 1.0 Sent to CCL by: David Shobe [shobedavid---gmail.com] --001a114e5fec44f33e05574e340b Content-Type: text/plain; charset="UTF-8" Is there such a thing as a .wfn to .wfx converter, so that I can use Firefly output as input for Aimall, when ECPs are used? On Aug 21, 2017 5:58 PM, "Zachary B Smithline zachary.smithline^^^yale.edu" wrote: Sent to CCL by: "Zachary B Smithline" [zachary.smithline_._yale.edu] Hi All, (I'm so sorry this is so long! Thank you so much, in advance!) I have been having serious issues optimizing and trying to run a 2D scan along two bond lengths for a ~200 atom protein active site, containing multiple Mg(II) atoms that have octahedral coordination in Gaussian 16. After relaxing the Hs at the AM1 level (holding everything else fixed), I relaxed all atoms in my system, holding only the backbone fixed. I noticed at this point that the octahedral coordination geometries of all Mg(II) atoms were distorted. Next, I started my relaxed scan along two bonds. However, every time I try the scan, Gaussian crashes and throws an error with the l103.exe. Using opt=calcfc or calcall does not help. Using smaller step sizes (like 0.01 or 0.05 A as opposed to 0.1) simply delays the inevitable crash. I have also tried repeating every step listed above using ONIOM B3LYP 6-31G(d)/AM1 where the Mg(II) and neighboring atoms are treated with DFT and everything else is treated with AM1. I still got the same error. This method is also too expensive and will not let me get the whole scan! *** MY QUESTIONS: 1. As a last ditch effort, I am trying to read in external AM1 parameters for Mg(II) (from this paper: J. Chem. Theory Comput. 2006, 2, 1050-1056) that were designed to reproduce octahedral coordination. Am1=MOPACExternal didn't work, so I want to use am1=input and read them in in Gaussian syntax. I have listed the external parameters from the paper below (in MOPAC syntax) and have also listed how I converted these parameters to Gaussian syntax. I have listed everything in Gaussian syntax except the HSP and GSP parameters because I don't understand the directions for how to write these in Gaussian syntax on the Gaussian info site. Does anybody know how to list HSP and GSP in Gaussian syntax? Here is what my parameter file that I link to in my Gaussian input has (HSP and GSP I haven't added yet): Method=8 CoreType=1 **** Mg U=12.83615,9.51125 Beta=1.26808,0.93230 ZetaOverlap=1.57114,1.25833 DCore=1.80310,1.99069,3.80477,0.66033,-0.00626,3.06817,1. 53666,-0.00581,2.33455,2.42691 Here are all the parameters I want to read in, in MOPAC format (reading it in this way didn't work): USS Mg 12.83615 UPP Mg 9.51125 BETAS Mg 1.26808 BETAP Mg 0.93230 ZS Mg 1.57114 ZP Mg 1.25833 ALP Mg 1.80310 FN11 Mg 1.99069 FN21 Mg 3.80477 FN31 Mg 0.66033 FN12 Mg 0.00626 FN22 Mg 3.06817 FN32 Mg 1.53666 FN13 Mg 0.00581 FN23 Mg 2.33455 FN33 Mg 2.42691 GSP Mg 8.29115 HSP Mg 0.53547 2. Do you have any other advice for my issue with the l103.exe error? Basically, I am trying to get a large 2D PE surface for my system at the AM1 level. Once I have this, I will refine the geometries/energies at each point on my surface in parallel at the DFT level at some national supercomputer. *** If anybody knows how to help, please contact me at zachary.smithline^-^ yale.edu Many thanks, Zachary Smithline Lab of Thomas Steitz Depts. of MB&B and Chemistry Yale Universityhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--001a114e5fec44f33e05574e340b Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Is there such a thing as a .wfn to .wfx converter, so tha= t I can use Firefly output as input for Aimall, when ECPs are used?

On Aug 21, 2017 5:5= 8 PM, "Zachary B Smithline zachary.smithline^^^yale.edu" <owne= r-chemistry*ccl.net> wrote:

Sent to CCL by: "Zachary B Smithline" [zachary.smithline_._yale.edu] Hi All,

(I'm so sorry this is so long!=C2=A0 Thank you so much, in advance!)
I have been having serious issues optimizing and trying to run a 2D scan al= ong two bond lengths
for a ~200 atom protein active site, containing multiple Mg(II) atoms that = have octahedral
coordination in Gaussian 16.=C2=A0 After relaxing the Hs at the AM1 level (= holding everything else fixed),
I relaxed all atoms in my system, holding only the backbone fixed. I notice= d at this point that the
octahedral coordination geometries of all Mg(II) atoms were distorted.

Next, I started my relaxed scan along two bonds.=C2=A0 However, every time = I try the scan, Gaussian
crashes and throws an error with the l103.exe.=C2=A0 Using opt=3Dcalcfc or = calcall does not help.=C2=A0 Using
smaller step sizes (like 0.01 or 0.05 A as opposed to 0.1) simply delays th= e inevitable crash.

I have also tried repeating every step listed above using ONIOM B3LYP 6-31G= (d)/AM1 where the
Mg(II) and neighboring atoms are treated with DFT and everything else is tr= eated with AM1.=C2=A0 I still
got the same error.=C2=A0 This method is also too expensive and will not le= t me get the whole scan!

***

MY QUESTIONS:

1. As a last ditch effort, I am trying to read in external AM1 parameters f= or Mg(II) (from this paper:
J. Chem. Theory Comput. 2006, 2, 1050-1056) that were designed to reproduce= octahedral
coordination.=C2=A0 Am1=3DMOPACExternal didn't work, so I want to use a= m1=3Dinput and read them in in
Gaussian syntax. I have listed the external parameters from the paper below= (in MOPAC syntax)
and have also listed how I converted these parameters to Gaussian syntax.= =C2=A0 I have listed
everything in Gaussian syntax except the HSP and GSP parameters because I d= on't understand
the directions for how to write these in Gaussian syntax on the Gaussian in= fo site.=C2=A0 Does anybody
know how to list HSP and GSP in Gaussian syntax?

Here is what my parameter file that I link to in my Gaussian input has (HSP= and GSP I haven't
added yet):

Method=3D8 CoreType=3D1
****
Mg
U=3D12.83615,9.51125
Beta=3D1.26808,0.93230
ZetaOverlap=3D1.57114,1.25833
DCore=3D1.80310,1.99069,3.80477,0.66033,-0.00626,3.06817,1.53666,= -0.00581,2.33455,2.42691

Here are all the parameters I want to read in, in MOPAC format (reading it = in this way didn't work):

USS=C2=A0 =C2=A0Mg=C2=A0 =C2=A012.83615
UPP=C2=A0 =C2=A0 Mg=C2=A0 =C2=A09.51125
BETAS=C2=A0 Mg=C2=A0 =C2=A01.26808
BETAP=C2=A0 Mg=C2=A0 =C2=A00.93230
ZS=C2=A0 =C2=A0 =C2=A0Mg=C2=A0 =C2=A0 1.57114
ZP=C2=A0 =C2=A0 =C2=A0Mg=C2=A0 =C2=A0 1.25833
ALP=C2=A0 =C2=A0 Mg=C2=A0 =C2=A0 1.80310
FN11=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 1.99069
FN21=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 3.80477
FN31=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 0.66033
FN12=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 0.00626
FN22=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 3.06817
FN32=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 1.53666
FN13=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 0.00581
FN23=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 2.33455
FN33=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 2.42691
GSP=C2=A0 =C2=A0 Mg=C2=A0 =C2=A0 8.29115
HSP=C2=A0 =C2=A0 Mg=C2=A0 =C2=A0 0.53547



2. Do you have any other advice for my issue with the l103.exe error?=C2=A0= Basically, I am trying to get
a large 2D PE surface for my system at the AM1 level. Once I have this, I w= ill refine the
geometries/energies at each point on my surface in parallel at the DFT leve= l at some national
supercomputer.

***

If anybody knows how to help, please contact me at zachary.smithline^-^yale.edu
Many thanks,
Zachary Smithline
Lab of Thomas Steitz
Depts. of MB&B and Chemistry
Yale University



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--001a114e5fec44f33e05574e340b-- From owner-chemistry@ccl.net Tue Aug 22 09:37:00 2017 From: "Norrby, Per-Ola Per-Ola.Norrby[]astrazeneca.com" To: CCL Subject: CCL:G: l103.exe error and reading in external AM1 parameters Message-Id: <-52942-170822010632-20417-ClZq7PBq6RP/1AZHSKqbyQ%a%server.ccl.net> X-Original-From: "Norrby, Per-Ola" Content-ID: <66857ECDD182D24BA8D8F0C724F1E9EB%a%AZCollaboration.onmicrosoft.com> Content-Language: sv-SE Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 22 Aug 2017 05:06:21 +0000 MIME-Version: 1.0 Sent to CCL by: "Norrby, Per-Ola" [Per-Ola.Norrby..astrazeneca.com] Dear Zachary, You're trying to fix the wave function, but I believe an l103 error is rather connected to a problem with the geometry definition. For geometry optimization, Gaussian represents your molecule by a number of bonds, angles, and torsions. If, during geometry optimization, an angle goes from nonlinear to linear, this causes some torsions to become undefined, causing a crash, fairly common. You might be able to simply restart from the point of the crash, in which case Gaussian might recognize the linear bend and set coordinates appropriately. However, I recommend trying to understand your coordinates and take control if them with "ModRedundant". Best regards, Per-Ola Sent from my iPhone > On 22 Aug 2017, at 00:04, Zachary B Smithline zachary.smithline^^^yale.edu wrote: > > > Sent to CCL by: "Zachary B Smithline" [zachary.smithline_._yale.edu] > Hi All, > > (I'm so sorry this is so long! Thank you so much, in advance!) > > I have been having serious issues optimizing and trying to run a 2D scan along two bond lengths > for a ~200 atom protein active site, containing multiple Mg(II) atoms that have octahedral > coordination in Gaussian 16. After relaxing the Hs at the AM1 level (holding everything else fixed), > I relaxed all atoms in my system, holding only the backbone fixed. I noticed at this point that the > octahedral coordination geometries of all Mg(II) atoms were distorted. > > Next, I started my relaxed scan along two bonds. However, every time I try the scan, Gaussian > crashes and throws an error with the l103.exe. Using opt=calcfc or calcall does not help. Using > smaller step sizes (like 0.01 or 0.05 A as opposed to 0.1) simply delays the inevitable crash. > > I have also tried repeating every step listed above using ONIOM B3LYP 6-31G(d)/AM1 where the > Mg(II) and neighboring atoms are treated with DFT and everything else is treated with AM1. I still > got the same error. This method is also too expensive and will not let me get the whole scan! > > *** > > MY QUESTIONS: > > 1. As a last ditch effort, I am trying to read in external AM1 parameters for Mg(II) (from this paper: > J. Chem. Theory Comput. 2006, 2, 1050-1056) that were designed to reproduce octahedral > coordination. Am1=MOPACExternal didn't work, so I want to use am1=input and read them in in > Gaussian syntax. I have listed the external parameters from the paper below (in MOPAC syntax) > and have also listed how I converted these parameters to Gaussian syntax. I have listed > everything in Gaussian syntax except the HSP and GSP parameters because I don't understand > the directions for how to write these in Gaussian syntax on the Gaussian info site. Does anybody > know how to list HSP and GSP in Gaussian syntax? > > Here is what my parameter file that I link to in my Gaussian input has (HSP and GSP I haven't > added yet): > > Method=8 CoreType=1 > **** > Mg > U=12.83615,9.51125 > Beta=1.26808,0.93230 > ZetaOverlap=1.57114,1.25833 > DCore=1.80310,1.99069,3.80477,0.66033,-0.00626,3.06817,1.53666,-0.00581,2.33455,2.42691 > > Here are all the parameters I want to read in, in MOPAC format (reading it in this way didn't work): > > USS Mg 12.83615 > UPP Mg 9.51125 > BETAS Mg 1.26808 > BETAP Mg 0.93230 > ZS Mg 1.57114 > ZP Mg 1.25833 > ALP Mg 1.80310 > FN11 Mg 1.99069 > FN21 Mg 3.80477 > FN31 Mg 0.66033 > FN12 Mg 0.00626 > FN22 Mg 3.06817 > FN32 Mg 1.53666 > FN13 Mg 0.00581 > FN23 Mg 2.33455 > FN33 Mg 2.42691 > GSP Mg 8.29115 > HSP Mg 0.53547 > > > > 2. Do you have any other advice for my issue with the l103.exe error? Basically, I am trying to get > a large 2D PE surface for my system at the AM1 level. Once I have this, I will refine the > geometries/energies at each point on my surface in parallel at the DFT level at some national > supercomputer. > > *** > > If anybody knows how to help, please contact me at zachary.smithline^-^yale.edu > > Many thanks, > Zachary Smithline > Lab of Thomas Steitz > Depts. of MB&B and Chemistry > Yale University> https://clicktime.symantec.com/a/1/UULPNIaluQR3HPPh8gcC8e-E2B-fz9PhOVgkYljadNk=?d=K2-LTKvY0KdXSIsPiMDsz2uQBSsohCf2aiF4JQM5clmaYa-JMApqZxKElcU6mGAg_as7dYBZ4tT4chGnXJfAOHYvsJNsGNdsTvyYloY6JQUjRmLvHzRN55b7m2a5eJcAZePOzB4TdsXSCkJ2nH3-t92ZZhqcw4om1jxc4jSXkk9SgnVqpPk2Dvpg9OV0-c9hX8jPYKlrtUtRFwmwaApOk1NECLF4mQUeRS5gRLbVrGfyhDxRWPq-FBt5ntLIFVXVqv5TocXpsHKpQrCYeh8jGHv6_dUeyOSRbG6rUCIZnJUYi5orNYzufut569X-joq8FjwJS2nRZuOEh5l0feUAiyzsRtVFVt17Lv4zRBnBCvsMlUbpNLGyszgMbk6-uPNfeXXHzd5conERnXXZCTHizav3c_RN9WFXQSwaflHPDw-OekUpeTndpPT2z4q6FkHpYH-yMKREb4MvgkBffiqPri7kN-HPIjXyUajeT00%3D&u=http%3A%2F%2Fwww.ccl.net%2Fcgi-bin%2Fccl%2Fsend_ccl_message> 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https://clicktime.symantec.com/a/1/EPRyO1Qn5RvIZ_C4jo7_SPumP6rTxUgmYcH4gbV4b5o=?d=K2-LTKvY0KdXSIsPiMDsz2uQBSsohCf2aiF4JQM5clmaYa-JMApqZxKElcU6mGAg_as7dYBZ4tT4chGnXJfAOHYvsJNsGNdsTvyYloY6JQUjRmLvHzRN55b7m2a5eJcAZePOzB4TdsXSCkJ2nH3-t92ZZhqcw4om1jxc4jSXkk9SgnVqpPk2Dvpg9OV0-c9hX8jPYKlrtUtRFwmwaApOk1NECLF4mQUeRS5gRLbVrGfyhDxRWPq-FBt5ntLIFVXVqv5TocXpsHKpQrCYeh8jGHv6_dUeyOSRbG6rUCIZnJUYi5orNYzufut569X-joq8FjwJS2nRZuOEh5l0feUAiyzsRtVFVt17Lv4zRBnBCvsMlUbpNLGyszgMbk6-uPNfeXXHzd5conERnXXZCTHizav3c_RN9WFXQSwaflHPDw-OekUpeTndpPT2z4q6FkHpYH-yMKREb4MvgkBffiqPri7kN-HPIjXyUajeT00%3D&u=http%3A%2F%2Fwww.ccl.net%2Fchemistry%2Faboutccl%2Finstructions%2F > > ________________________________ Confidentiality Notice: This message is private and may contain confidential and proprietary information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorized use or disclosure of the contents of this message is not permitted and may be unlawful. From owner-chemistry@ccl.net Tue Aug 22 10:12:00 2017 From: "Adam Tenderholt atenderholt|a|gmail.com" To: CCL Subject: CCL:G: Wfn to wfx converter? Message-Id: <-52943-170822100948-13500-2eICvP5TtPdbrgB/YkhRcw##server.ccl.net> X-Original-From: Adam Tenderholt Content-Type: multipart/alternative; boundary="94eb2c1af8486b704505575825b9" Date: Tue, 22 Aug 2017 14:09:29 +0000 MIME-Version: 1.0 Sent to CCL by: Adam Tenderholt [atenderholt(-)gmail.com] --94eb2c1af8486b704505575825b9 Content-Type: text/plain; charset="UTF-8" Hi David, As part of Google Summer of Code, the cclib project has a student working on a WFX writer. You should be able to take Firefly output and convert to WFX directly, without going through WFN. Here's a link to the Python code: https://github.com/gaursagar/cclib/tree/wfx-writer. Once installed, you should be able to use the ccwrite script for the conversion. Let me know if you have questions or need help installing cclib. Adam On Tue, Aug 22, 2017 at 7:01 AM David Shobe shobedavid]![gmail.com < owner-chemistry..ccl.net> wrote: > Is there such a thing as a .wfn to .wfx converter, so that I can use > Firefly output as input for Aimall, when ECPs are used? > > On Aug 21, 2017 5:58 PM, "Zachary B Smithline zachary.smithline^^^yale.edu > " > wrote: > > > Sent to CCL by: "Zachary B Smithline" [zachary.smithline_._yale.edu] > Hi All, > > (I'm so sorry this is so long! Thank you so much, in advance!) > > I have been having serious issues optimizing and trying to run a 2D scan > along two bond lengths > for a ~200 atom protein active site, containing multiple Mg(II) atoms that > have octahedral > coordination in Gaussian 16. After relaxing the Hs at the AM1 level > (holding everything else fixed), > I relaxed all atoms in my system, holding only the backbone fixed. I > noticed at this point that the > octahedral coordination geometries of all Mg(II) atoms were distorted. > > Next, I started my relaxed scan along two bonds. However, every time I try > the scan, Gaussian > crashes and throws an error with the l103.exe. Using opt=calcfc or calcall > does not help. Using > smaller step sizes (like 0.01 or 0.05 A as opposed to 0.1) simply delays > the inevitable crash. > > I have also tried repeating every step listed above using ONIOM B3LYP > 6-31G(d)/AM1 where the > Mg(II) and neighboring atoms are treated with DFT and everything else is > treated with AM1. I still > got the same error. This method is also too expensive and will not let me > get the whole scan! > > *** > > MY QUESTIONS: > > 1. As a last ditch effort, I am trying to read in external AM1 parameters > for Mg(II) (from this paper: > J. Chem. Theory Comput. 2006, 2, 1050-1056) that were designed to reproduce > octahedral > coordination. Am1=MOPACExternal didn't work, so I want to use am1=input > and read them in in > Gaussian syntax. I have listed the external parameters from the paper below > (in MOPAC syntax) > and have also listed how I converted these parameters to Gaussian syntax. > I have listed > everything in Gaussian syntax except the HSP and GSP parameters because I > don't understand > the directions for how to write these in Gaussian syntax on the Gaussian > info site. Does anybody > know how to list HSP and GSP in Gaussian syntax? > > Here is what my parameter file that I link to in my Gaussian input has (HSP > and GSP I haven't > added yet): > > Method=8 CoreType=1 > **** > Mg > U=12.83615,9.51125 > Beta=1.26808,0.93230 > ZetaOverlap=1.57114,1.25833 > DCore=1.80310,1.99069,3.80477,0.66033,-0.00626,3.06817,1. > 53666,-0.00581,2.33455,2.42691 > > Here are all the parameters I want to read in, in MOPAC format (reading it > in this way didn't work): > > USS Mg 12.83615 > UPP Mg 9.51125 > BETAS Mg 1.26808 > BETAP Mg 0.93230 > ZS Mg 1.57114 > ZP Mg 1.25833 > ALP Mg 1.80310 > FN11 Mg 1.99069 > FN21 Mg 3.80477 > FN31 Mg 0.66033 > FN12 Mg 0.00626 > FN22 Mg 3.06817 > FN32 Mg 1.53666 > FN13 Mg 0.00581 > FN23 Mg 2.33455 > FN33 Mg 2.42691 > GSP Mg 8.29115 > HSP Mg 0.53547 > > > > 2. Do you have any other advice for my issue with the l103.exe error? > Basically, I am trying to get > a large 2D PE surface for my system at the AM1 level. Once I have this, I > will refine the > geometries/energies at each point on my surface in parallel at the DFT > level at some national > supercomputer. > > *** > > If anybody knows how to help, please contact me at zachary.smithline^-^ > yale.edu > > Many thanks, > Zachary Smithline > Lab of Thomas Steitz > Depts. of MB&B and Chemistry > Yale Universityhttp:// > www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--001a114e5fec44f33e05574e340b > Content-Type > : > text/html; charset="UTF-8" > Content-Transfer-Encoding: quoted-printable > >
Is there such a thing as a .wfn to .wfx converter, so > tha= > t I can use Firefly output as input for Aimall, when ECPs are > used?
iv class=3D"gmail_extra">
On Aug 21, 2017 > 5:5= > 8 PM, "Zachary B Smithline zachary.smithline^^^ http://yale.= > edu">yale.edu" < ">owne= > r-chemistry[*]ccl.net> wrote:
clas= > s=3D"quote" style=3D"margin:0 0 0 .8ex;border-left:1px #ccc > solid;padding-l= > eft:1ex">
> Sent to CCL by: "Zachary B Smithline" [zachary.smithline_._ hre= > f=3D"http://yale.edu" rel=3D"noreferrer" target=3D"_blank">yale.edu > ] > > Hi All,
>
> (I'm so sorry this is so long!=C2=A0 Thank you so much, in > advance!) > >
> I have been having serious issues optimizing and trying to run a 2D scan > al= > ong two bond lengths
> for a ~200 atom protein active site, containing multiple Mg(II) atoms that > = > have octahedral
> coordination in Gaussian 16.=C2=A0 After relaxing the Hs at the AM1 level > (= > holding everything else fixed),
> I relaxed all atoms in my system, holding only the backbone fixed. I > notice= > d at this point that the
> octahedral coordination geometries of all Mg(II) atoms were distorted.
>
> Next, I started my relaxed scan along two bonds.=C2=A0 However, every time > = > I try the scan, Gaussian
> crashes and throws an error with the l103.exe.=C2=A0 Using opt=3Dcalcfc or > = > calcall does not help.=C2=A0 Using
> smaller step sizes (like 0.01 or 0.05 A as opposed to 0.1) simply delays > th= > e inevitable crash.
>
> I have also tried repeating every step listed above using ONIOM B3LYP > 6-31G= > (d)/AM1 where the
> Mg(II) and neighboring atoms are treated with DFT and everything else is > tr= > eated with AM1.=C2=A0 I still
> got the same error.=C2=A0 This method is also too expensive and will not > le= > t me get the whole scan!
>
> ***
>
> MY QUESTIONS:
>
> 1. As a last ditch effort, I am trying to read in external AM1 parameters > f= > or Mg(II) (from this paper:
> J. Chem. Theory Comput. 2006, 2, 1050-1056) that were designed to > reproduce= > octahedral
> coordination.=C2=A0 Am1=3DMOPACExternal didn't work, so I want to use > a= > m1=3Dinput and read them in in
> Gaussian syntax. I have listed the external parameters from the paper > below= > (in MOPAC syntax)
> and have also listed how I converted these parameters to Gaussian syntax.= > =C2=A0 I have listed
> everything in Gaussian syntax except the HSP and GSP parameters because I > d= > on't understand
> the directions for how to write these in Gaussian syntax on the Gaussian > in= > fo site.=C2=A0 Does anybody
> know how to list HSP and GSP in Gaussian syntax?
>
> Here is what my parameter file that I link to in my Gaussian input has > (HSP= > and GSP I haven't
> added yet):
>
> Method=3D8 CoreType=3D1
> ****
> Mg
> U=3D12.83615,9.51125
> Beta=3D1.26808,0.93230
> ZetaOverlap=3D1.57114,1.25833
> > DCore=3D1.80310,1.99069,3.80477,0.66033,-0.00626,3.06817,1.53666,= > -0.00581,2.33455,2.42691
>
> Here are all the parameters I want to read in, in MOPAC format (reading it > = > in this way didn't work):
>
> USS=C2=A0 =C2=A0Mg=C2=A0 =C2=A012.83615
> UPP=C2=A0 =C2=A0 Mg=C2=A0 =C2=A09.51125
> BETAS=C2=A0 Mg=C2=A0 =C2=A01.26808
> BETAP=C2=A0 Mg=C2=A0 =C2=A00.93230
> ZS=C2=A0 =C2=A0 =C2=A0Mg=C2=A0 =C2=A0 1.57114
> ZP=C2=A0 =C2=A0 =C2=A0Mg=C2=A0 =C2=A0 1.25833
> ALP=C2=A0 =C2=A0 Mg=C2=A0 =C2=A0 1.80310
> FN11=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 1.99069
> FN21=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 3.80477
> FN31=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 0.66033
> FN12=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 0.00626
> FN22=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 3.06817
> FN32=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 1.53666
> FN13=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 0.00581
> FN23=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 2.33455
> FN33=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 2.42691
> GSP=C2=A0 =C2=A0 Mg=C2=A0 =C2=A0 8.29115
> HSP=C2=A0 =C2=A0 Mg=C2=A0 =C2=A0 0.53547
>
>
>
> 2. Do you have any other advice for my issue with the l103.exe > error?=C2=A0= > Basically, I am trying to get
> a large 2D PE surface for my system at the AM1 level. Once I have this, I > w= > ill refine the
> geometries/energies at each point on my surface in parallel at the DFT > leve= > l at some national
> supercomputer.
>
> ***
>
> If anybody knows how to help, please contact me at zachary.smithline^-^ h= > ref=3D"http://yale.edu" rel=3D"noreferrer" target=3D"_blank">yale.edu > r> >
> Many thanks,
> Zachary Smithline
> Lab of Thomas Steitz
> Depts. of MB&B and Chemistry
> Yale University
>
>
>
> -=3D This is automatically added to each message by the mailing script > =3D-= > >
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>
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>

> --94eb2c1af8486b704505575825b9 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi David,

As part of Google Summer of C= ode, the cclib project has a student working on a WFX writer. You should be= able to take Firefly output and convert to WFX directly, without going thr= ough WFN.

Here's a link to the Python code:=C2= =A0https://g= ithub.com/gaursagar/cclib/tree/wfx-writer. Once installed, you should b= e able to use the ccwrite script for the conversion.

Let me know if you have questions or need help installing cclib.

Adam


On Tue, Aug 22, 2017 at 7:01 AM David Sho= be shobedavid]![gmail.com <owner-chemistry..ccl.net> wrote:
Is there such a thing as a .wfn to .wfx = converter, so that I can use
Firefly output as input for Aimall, when ECPs are used?

On Aug 21, 2017 5:58 PM, "Zachary B Smithline zachary.smithline^^^yale.edu&q= uot;
<owner-chemistry[*]ccl.net> wrote:


Sent to CCL by: "Zachary B Smithline" [zachary.smithline_._yale.edu] Hi All,

(I'm so sorry this is so long!=C2=A0 Thank you so much, in advance!)
I have been having serious issues optimizing and trying to run a 2D scan along two bond lengths
for a ~200 atom protein active site, containing multiple Mg(II) atoms that<= br> have octahedral
coordination in Gaussian 16.=C2=A0 After relaxing the Hs at the AM1 level (holding everything else fixed),
I relaxed all atoms in my system, holding only the backbone fixed. I
noticed at this point that the
octahedral coordination geometries of all Mg(II) atoms were distorted.

Next, I started my relaxed scan along two bonds.=C2=A0 However, every time = I try
the scan, Gaussian
crashes and throws an error with the l103.exe.=C2=A0 Using opt=3Dcalcfc or = calcall
does not help.=C2=A0 Using
smaller step sizes (like 0.01 or 0.05 A as opposed to 0.1) simply delays the inevitable crash.

I have also tried repeating every step listed above using ONIOM B3LYP
6-31G(d)/AM1 where the
Mg(II) and neighboring atoms are treated with DFT and everything else is treated with AM1.=C2=A0 I still
got the same error.=C2=A0 This method is also too expensive and will not le= t me
get the whole scan!

***

MY QUESTIONS:

1. As a last ditch effort, I am trying to read in external AM1 parameters for Mg(II) (from this paper:
J. Chem. Theory Comput. 2006, 2, 1050-1056) that were designed to reproduce=
octahedral
coordination.=C2=A0 Am1=3DMOPACExternal didn't work, so I want to use a= m1=3Dinput
and read them in in
Gaussian syntax. I have listed the external parameters from the paper below=
(in MOPAC syntax)
and have also listed how I converted these parameters to Gaussian syntax. I have listed
everything in Gaussian syntax except the HSP and GSP parameters because I don't understand
the directions for how to write these in Gaussian syntax on the Gaussian info site.=C2=A0 Does anybody
know how to list HSP and GSP in Gaussian syntax?

Here is what my parameter file that I link to in my Gaussian input has (HSP=
and GSP I haven't
added yet):

Method=3D8 CoreType=3D1
****
Mg
U=3D12.83615,9.51125
Beta=3D1.26808,0.93230
ZetaOverlap=3D1.57114,1.25833
DCore=3D1.80310,1.99069,3.80477,0.66033,-0.00626,3.06817,1.
53666,-0.00581,2.33455,2.42691

Here are all the parameters I want to read in, in MOPAC format (reading it<= br> in this way didn't work):

USS=C2=A0 =C2=A0Mg=C2=A0 =C2=A012.83615
UPP=C2=A0 =C2=A0 Mg=C2=A0 =C2=A09.51125
BETAS=C2=A0 Mg=C2=A0 =C2=A01.26808
BETAP=C2=A0 Mg=C2=A0 =C2=A00.93230
ZS=C2=A0 =C2=A0 =C2=A0Mg=C2=A0 =C2=A0 1.57114
ZP=C2=A0 =C2=A0 =C2=A0Mg=C2=A0 =C2=A0 1.25833
ALP=C2=A0 =C2=A0 Mg=C2=A0 =C2=A0 1.80310
FN11=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 1.99069
FN21=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 3.80477
FN31=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 0.66033
FN12=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 0.00626
FN22=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 3.06817
FN32=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 1.53666
FN13=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 0.00581
FN23=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 2.33455
FN33=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 2.42691
GSP=C2=A0 =C2=A0 Mg=C2=A0 =C2=A0 8.29115
HSP=C2=A0 =C2=A0 Mg=C2=A0 =C2=A0 0.53547



2. Do you have any other advice for my issue with the l103.exe error?
Basically, I am trying to get
a large 2D PE surface for my system at the AM1 level. Once I have this, I will refine the
geometries/energies at each point on my surface in parallel at the DFT
level at some national
supercomputer.

***

If anybody knows how to help, please contact me at zachary.smithline^-^
yale.edu

Many thanks,
Zachary Smithline
Lab of Thomas Steitz
Depts. of MB&B and Chemistry
Yale Universityhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chem= istry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--001a114e5fec44f33e055= 74e340b
Content-Type: text/html; charset=3D"UTF-8"
Content-Transfer-Encoding: quoted-printable

<div dir=3D3D"auto">Is there such a thing as a .wfn to .wfx= converter, so tha=3D
t I can use Firefly output as input for Aimall, when ECPs are used?</div= ><d=3D
iv class=3D3D"gmail_extra"><br><div class=3D3D"g= mail_quote">On Aug 21, 2017 5:5=3D
8 PM, &quot;Zachary B Smithline zachary.smithline^^^<a href=3D3D&quo= t;http://yale= .=3D
edu">yale.edu</a>&quot; &lt;<a href=3D3D"mailto:owner-chemistry[*]ccl.net&qu= ot;>owne=3D
r-chemistry[*]ccl.net</a>&gt; wrote:<br type=3D3D"attribution&qu= ot;><blockquote clas=3D
s=3D3D"quote" style=3D3D"margin:0 0 0 .8ex;border-left:1px #= ccc solid;padding-l=3D
eft:1ex"><br>
Sent to CCL by: &quot;Zachary B Smithline&quot; [zachary.smithline_= ._<a hre=3D
f=3D3D"http://yale.edu" rel=3D3D"noreferrer" target=3D3D"= ;_blank">yale.edu</a>]<br=3D
>
Hi All,<br>
<br>
(I&#39;m so sorry this is so long!=3DC2=3DA0 Thank you so much, in adva= nce!)<br=3D
>
<br>
I have been having serious issues optimizing and trying to run a 2D scan al= =3D
ong two bond lengths<br>
for a ~200 atom protein active site, containing multiple Mg(II) atoms that = =3D
have octahedral<br>
coordination in Gaussian 16.=3DC2=3DA0 After relaxing the Hs at the AM1 lev= el (=3D
holding everything else fixed),<br>
I relaxed all atoms in my system, holding only the backbone fixed. I notice= =3D
d at this point that the<br>
octahedral coordination geometries of all Mg(II) atoms were distorted.<b= r>
<br>
Next, I started my relaxed scan along two bonds.=3DC2=3DA0 However, every t= ime =3D
I try the scan, Gaussian<br>
crashes and throws an error with the l103.exe.=3DC2=3DA0 Using opt=3D3Dcalc= fc or =3D
calcall does not help.=3DC2=3DA0 Using<br>
smaller step sizes (like 0.01 or 0.05 A as opposed to 0.1) simply delays th= =3D
e inevitable crash.<br>
<br>
I have also tried repeating every step listed above using ONIOM B3LYP 6-31G= =3D
(d)/AM1 where the<br>
Mg(II) and neighboring atoms are treated with DFT and everything else is tr= =3D
eated with AM1.=3DC2=3DA0 I still<br>
got the same error.=3DC2=3DA0 This method is also too expensive and will no= t le=3D
t me get the whole scan!<br>
<br>
***<br>
<br>
MY QUESTIONS:<br>
<br>
1. As a last ditch effort, I am trying to read in external AM1 parameters f= =3D
or Mg(II) (from this paper:<br>
J. Chem. Theory Comput. 2006, 2, 1050-1056) that were designed to reproduce= =3D
=C2=A0octahedral<br>
coordination.=3DC2=3DA0 Am1=3D3DMOPACExternal didn&#39;t work, so I wan= t to use a=3D
m1=3D3Dinput and read them in in<br>
Gaussian syntax. I have listed the external parameters from the paper below= =3D
=C2=A0(in MOPAC syntax)<br>
and have also listed how I converted these parameters to Gaussian syntax.= =3D
=3DC2=3DA0 I have listed<br>
everything in Gaussian syntax except the HSP and GSP parameters because I d= =3D
on&#39;t understand<br>
the directions for how to write these in Gaussian syntax on the Gaussian in= =3D
fo site.=3DC2=3DA0 Does anybody<br>
know how to list HSP and GSP in Gaussian syntax?<br>
<br>
Here is what my parameter file that I link to in my Gaussian input has (HSP= =3D
=C2=A0and GSP I haven&#39;t<br>
added yet):<br>
<br>
Method=3D3D8 CoreType=3D3D1<br>
****<br>
Mg<br>
U=3D3D12.83615,9.51125<br>
Beta=3D3D1.26808,0.93230<br>
ZetaOverlap=3D3D1.57114,1.25833<br>
DCore=3D3D1.80310,1.99069,3.80477,<wbr>0.66033,-0.00626,3.06817,1.<= ;wbr>53666,=3D
-0.00581,2.33455,2.42691<br>
<br>
Here are all the parameters I want to read in, in MOPAC format (reading it = =3D
in this way didn&#39;t work):<br>
<br>
USS=3DC2=3DA0 =3DC2=3DA0Mg=3DC2=3DA0 =3DC2=3DA012.83615<br>
UPP=3DC2=3DA0 =3DC2=3DA0 Mg=3DC2=3DA0 =3DC2=3DA09.51125<br>
BETAS=3DC2=3DA0 Mg=3DC2=3DA0 =3DC2=3DA01.26808<br>
BETAP=3DC2=3DA0 Mg=3DC2=3DA0 =3DC2=3DA00.93230<br>
ZS=3DC2=3DA0 =3DC2=3DA0 =3DC2=3DA0Mg=3DC2=3DA0 =3DC2=3DA0 1.57114<br>=
ZP=3DC2=3DA0 =3DC2=3DA0 =3DC2=3DA0Mg=3DC2=3DA0 =3DC2=3DA0 1.25833<br>=
ALP=3DC2=3DA0 =3DC2=3DA0 Mg=3DC2=3DA0 =3DC2=3DA0 1.80310<br>
FN11=3DC2=3DA0 =3DC2=3DA0Mg=3DC2=3DA0 =3DC2=3DA0 1.99069<br>
FN21=3DC2=3DA0 =3DC2=3DA0Mg=3DC2=3DA0 =3DC2=3DA0 3.80477<br>
FN31=3DC2=3DA0 =3DC2=3DA0Mg=3DC2=3DA0 =3DC2=3DA0 0.66033<br>
FN12=3DC2=3DA0 =3DC2=3DA0Mg=3DC2=3DA0 =3DC2=3DA0 0.00626<br>
FN22=3DC2=3DA0 =3DC2=3DA0Mg=3DC2=3DA0 =3DC2=3DA0 3.06817<br>
FN32=3DC2=3DA0 =3DC2=3DA0Mg=3DC2=3DA0 =3DC2=3DA0 1.53666<br>
FN13=3DC2=3DA0 =3DC2=3DA0Mg=3DC2=3DA0 =3DC2=3DA0 0.00581<br>
FN23=3DC2=3DA0 =3DC2=3DA0Mg=3DC2=3DA0 =3DC2=3DA0 2.33455<br>
FN33=3DC2=3DA0 =3DC2=3DA0Mg=3DC2=3DA0 =3DC2=3DA0 2.42691<br>
GSP=3DC2=3DA0 =3DC2=3DA0 Mg=3DC2=3DA0 =3DC2=3DA0 8.29115<br>
HSP=3DC2=3DA0 =3DC2=3DA0 Mg=3DC2=3DA0 =3DC2=3DA0 0.53547<br>
<br>
<br>
<br>
2. Do you have any other advice for my issue with the l103.exe error?=3DC2= =3DA0=3D
=C2=A0Basically, I am trying to get<br>
a large 2D PE surface for my system at the AM1 level. Once I have this, I w= =3D
ill refine the<br>
geometries/energies at each point on my surface in parallel at the DFT leve= =3D
l at some national<br>
supercomputer.<br>
<br>
***<br>
<br>
If anybody knows how to help, please contact me at zachary.smithline^-^<= a h=3D
ref=3D3D"http://yale.edu" rel=3D3D"noreferrer" target=3D3D&qu= ot;_blank">yale.edu</a><b=3D
r>
<br>
Many thanks,<br>
Zachary Smithline<br>
Lab of Thomas Steitz<br>
Depts. of MB&amp;B and Chemistry<br>
Yale University<br>
<br>
<br>
<br>
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--94eb2c1af8486b704505575825b9-- From owner-chemistry@ccl.net Tue Aug 22 11:29:00 2017 From: "=?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal victor]=[fluor.quimica.uniovi.es" To: CCL Subject: CCL:G: Wfn to wfx converter? Message-Id: <-52944-170822112620-32095-KbDFAkyiaxtMya9zaef0xw|*|server.ccl.net> X-Original-From: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Tue, 22 Aug 2017 16:48:24 +0200 MIME-Version: 1.0 Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor.:.fluor.quimica.uniovi.es] On Mon, Aug 21, 2017 at 09:17:59PM -0500, David Shobe shobedavid]![gmail.com wrote: > Is there such a thing as a .wfn to .wfx converter, so that I can use > Firefly output as input for Aimall, when ECPs are used? Maybe you can recover the results from the *.chk or *.fchk and ask gaussian to write the *.wfx. Not a wfn2wfx converter but it achieves the same. Regards, Dr. Víctor Luaña -- . . "Half of the US people use twitter to form its opinion and half / `' \ also elect the US president. I only hope they are not the same /(o)(o)\ half". --From a sentence by Gore Vidal /`. \/ .'\ / '`'` \ "[Technocrats, academics and journalists} are often motivated | \'`'`/ | by hope while the public at large tends to be more focused | |'`'`| | on fear." -- Russell Mead (The Washington Post, 2017) \/`'`'`'\/ ==(((==)))===================================+=========================== ! Dr.Víctor Luaña, in silico chemist & prof. ! ! Departamento de Química Física y Analítica ! ! Universidad de Oviedo, 33006-Oviedo, Spain ! ! e-mail: ! ! phone: +34-985-103491 fax: +34-985-103125 ! +--------------------------------------------+ GroupPage: Articles: git-hub: ORCID: 0000-0003-4585-4627; RID: H-2045-2015 From owner-chemistry@ccl.net Tue Aug 22 15:27:01 2017 From: "Felipe Schneider schneider.felipe.5_-_gmail.com" To: CCL Subject: CCL:G: Wfn to wfx converter? Message-Id: <-52945-170822112315-30474-qnFGuHQYivgPpzzCA9hPVQ!A!server.ccl.net> X-Original-From: Felipe Schneider Content-Type: multipart/alternative; boundary="94eb2c1cde9a2689aa0557592cdf" Date: Tue, 22 Aug 2017 15:22:57 +0000 MIME-Version: 1.0 Sent to CCL by: Felipe Schneider [schneider.felipe.5#gmail.com] --94eb2c1cde9a2689aa0557592cdf Content-Type: text/plain; charset="UTF-8" Dear David, If you can generate a .molden file, Molden2AIM might work for you: < https://github.com/zorkzou/Molden2AIM>. All the best, Felipe On Tue, 22 Aug 2017 at 12:08 David Shobe shobedavid]![gmail.com < owner-chemistry*o*ccl.net> wrote: > Is there such a thing as a .wfn to .wfx converter, so that I can use > Firefly output as input for Aimall, when ECPs are used? > > On Aug 21, 2017 5:58 PM, "Zachary B Smithline zachary.smithline^^^yale.edu > " > wrote: > > > Sent to CCL by: "Zachary B Smithline" [zachary.smithline_._yale.edu] > Hi All, > > (I'm so sorry this is so long! Thank you so much, in advance!) > > I have been having serious issues optimizing and trying to run a 2D scan > along two bond lengths > for a ~200 atom protein active site, containing multiple Mg(II) atoms that > have octahedral > coordination in Gaussian 16. After relaxing the Hs at the AM1 level > (holding everything else fixed), > I relaxed all atoms in my system, holding only the backbone fixed. I > noticed at this point that the > octahedral coordination geometries of all Mg(II) atoms were distorted. > > Next, I started my relaxed scan along two bonds. However, every time I try > the scan, Gaussian > crashes and throws an error with the l103.exe. Using opt=calcfc or calcall > does not help. Using > smaller step sizes (like 0.01 or 0.05 A as opposed to 0.1) simply delays > the inevitable crash. > > I have also tried repeating every step listed above using ONIOM B3LYP > 6-31G(d)/AM1 where the > Mg(II) and neighboring atoms are treated with DFT and everything else is > treated with AM1. I still > got the same error. This method is also too expensive and will not let me > get the whole scan! > > *** > > MY QUESTIONS: > > 1. As a last ditch effort, I am trying to read in external AM1 parameters > for Mg(II) (from this paper: > J. Chem. Theory Comput. 2006, 2, 1050-1056) that were designed to reproduce > octahedral > coordination. Am1=MOPACExternal didn't work, so I want to use am1=input > and read them in in > Gaussian syntax. I have listed the external parameters from the paper below > (in MOPAC syntax) > and have also listed how I converted these parameters to Gaussian syntax. > I have listed > everything in Gaussian syntax except the HSP and GSP parameters because I > don't understand > the directions for how to write these in Gaussian syntax on the Gaussian > info site. Does anybody > know how to list HSP and GSP in Gaussian syntax? > > Here is what my parameter file that I link to in my Gaussian input has (HSP > and GSP I haven't > added yet): > > Method=8 CoreType=1 > **** > Mg > U=12.83615,9.51125 > Beta=1.26808,0.93230 > ZetaOverlap=1.57114,1.25833 > DCore=1.80310,1.99069,3.80477,0.66033,-0.00626,3.06817,1. > 53666,-0.00581,2.33455,2.42691 > > Here are all the parameters I want to read in, in MOPAC format (reading it > in this way didn't work): > > USS Mg 12.83615 > UPP Mg 9.51125 > BETAS Mg 1.26808 > BETAP Mg 0.93230 > ZS Mg 1.57114 > ZP Mg 1.25833 > ALP Mg 1.80310 > FN11 Mg 1.99069 > FN21 Mg 3.80477 > FN31 Mg 0.66033 > FN12 Mg 0.00626 > FN22 Mg 3.06817 > FN32 Mg 1.53666 > FN13 Mg 0.00581 > FN23 Mg 2.33455 > FN33 Mg 2.42691 > GSP Mg 8.29115 > HSP Mg 0.53547 > > > > 2. Do you have any other advice for my issue with the l103.exe error? > Basically, I am trying to get > a large 2D PE surface for my system at the AM1 level. Once I have this, I > will refine the > geometries/energies at each point on my surface in parallel at the DFT > level at some national > supercomputer. > > *** > > If anybody knows how to help, please contact me at zachary.smithline^-^ > yale.edu > > Many thanks, > Zachary Smithline > Lab of Thomas Steitz > Depts. of MB&B and Chemistry > Yale Universityhttp:// > www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--001a114e5fec44f33e05574e340b > Content-Type > : > text/html; charset="UTF-8" > Content-Transfer-Encoding: quoted-printable > >
Is there such a thing as a .wfn to .wfx converter, so > tha= > t I can use Firefly output as input for Aimall, when ECPs are > used?
iv class=3D"gmail_extra">
On Aug 21, 2017 > 5:5= > 8 PM, "Zachary B Smithline zachary.smithline^^^ http://yale.= > edu">yale.edu" < ">owne= > r-chemistry[*]ccl.net> wrote:
clas= > s=3D"quote" style=3D"margin:0 0 0 .8ex;border-left:1px #ccc > solid;padding-l= > eft:1ex">
> Sent to CCL by: "Zachary B Smithline" [zachary.smithline_._ hre= > f=3D"http://yale.edu" rel=3D"noreferrer" target=3D"_blank">yale.edu > ] > > Hi All,
>
> (I'm so sorry this is so long!=C2=A0 Thank you so much, in > advance!) > >
> I have been having serious issues optimizing and trying to run a 2D scan > al= > ong two bond lengths
> for a ~200 atom protein active site, containing multiple Mg(II) atoms that > = > have octahedral
> coordination in Gaussian 16.=C2=A0 After relaxing the Hs at the AM1 level > (= > holding everything else fixed),
> I relaxed all atoms in my system, holding only the backbone fixed. I > notice= > d at this point that the
> octahedral coordination geometries of all Mg(II) atoms were distorted.
>
> Next, I started my relaxed scan along two bonds.=C2=A0 However, every time > = > I try the scan, Gaussian
> crashes and throws an error with the l103.exe.=C2=A0 Using opt=3Dcalcfc or > = > calcall does not help.=C2=A0 Using
> smaller step sizes (like 0.01 or 0.05 A as opposed to 0.1) simply delays > th= > e inevitable crash.
>
> I have also tried repeating every step listed above using ONIOM B3LYP > 6-31G= > (d)/AM1 where the
> Mg(II) and neighboring atoms are treated with DFT and everything else is > tr= > eated with AM1.=C2=A0 I still
> got the same error.=C2=A0 This method is also too expensive and will not > le= > t me get the whole scan!
>
> ***
>
> MY QUESTIONS:
>
> 1. As a last ditch effort, I am trying to read in external AM1 parameters > f= > or Mg(II) (from this paper:
> J. Chem. Theory Comput. 2006, 2, 1050-1056) that were designed to > reproduce= > octahedral
> coordination.=C2=A0 Am1=3DMOPACExternal didn't work, so I want to use > a= > m1=3Dinput and read them in in
> Gaussian syntax. I have listed the external parameters from the paper > below= > (in MOPAC syntax)
> and have also listed how I converted these parameters to Gaussian syntax.= > =C2=A0 I have listed
> everything in Gaussian syntax except the HSP and GSP parameters because I > d= > on't understand
> the directions for how to write these in Gaussian syntax on the Gaussian > in= > fo site.=C2=A0 Does anybody
> know how to list HSP and GSP in Gaussian syntax?
>
> Here is what my parameter file that I link to in my Gaussian input has > (HSP= > and GSP I haven't
> added yet):
>
> Method=3D8 CoreType=3D1
> ****
> Mg
> U=3D12.83615,9.51125
> Beta=3D1.26808,0.93230
> ZetaOverlap=3D1.57114,1.25833
> > DCore=3D1.80310,1.99069,3.80477,0.66033,-0.00626,3.06817,1.53666,= > -0.00581,2.33455,2.42691
>
> Here are all the parameters I want to read in, in MOPAC format (reading it > = > in this way didn't work):
>
> USS=C2=A0 =C2=A0Mg=C2=A0 =C2=A012.83615
> UPP=C2=A0 =C2=A0 Mg=C2=A0 =C2=A09.51125
> BETAS=C2=A0 Mg=C2=A0 =C2=A01.26808
> BETAP=C2=A0 Mg=C2=A0 =C2=A00.93230
> ZS=C2=A0 =C2=A0 =C2=A0Mg=C2=A0 =C2=A0 1.57114
> ZP=C2=A0 =C2=A0 =C2=A0Mg=C2=A0 =C2=A0 1.25833
> ALP=C2=A0 =C2=A0 Mg=C2=A0 =C2=A0 1.80310
> FN11=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 1.99069
> FN21=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 3.80477
> FN31=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 0.66033
> FN12=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 0.00626
> FN22=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 3.06817
> FN32=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 1.53666
> FN13=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 0.00581
> FN23=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 2.33455
> FN33=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 2.42691
> GSP=C2=A0 =C2=A0 Mg=C2=A0 =C2=A0 8.29115
> HSP=C2=A0 =C2=A0 Mg=C2=A0 =C2=A0 0.53547
>
>
>
> 2. Do you have any other advice for my issue with the l103.exe > error?=C2=A0= > Basically, I am trying to get
> a large 2D PE surface for my system at the AM1 level. Once I have this, I > w= > ill refine the
> geometries/energies at each point on my surface in parallel at the DFT > leve= > l at some national
> supercomputer.
>
> ***
>
> If anybody knows how to help, please contact me at zachary.smithline^-^ h= > ref=3D"http://yale.edu" rel=3D"noreferrer" target=3D"_blank">yale.edu > r> >
> Many thanks,
> Zachary Smithline
> Lab of Thomas Steitz
> Depts. of MB&B and Chemistry
> Yale University
>
>
>
> -=3D This is automatically added to each message by the mailing script > =3D-= > >
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> --94eb2c1cde9a2689aa0557592cdf Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear David,

If you can generate a .mold= en file, Molden2AIM might work for you: <https://github.com/zorkzou/Molden2AIM>.

All the best,
Felipe

On Tue, 22 Aug 2017 at 12:08 David Shobe sho= bedavid]![gmail.com <owner-chemistry*o*ccl.net> wrote:
Is there such a thing as a .wfn to .wfx conver= ter, so that I can use
Firefly output as input for Aimall, when ECPs are used?

On Aug 21, 2017 5:58 PM, "Zachary B Smithline zachary.smithline^^^yale.edu&q= uot;
<owner-chemistry[*]ccl.net> wrote:


Sent to CCL by: "Zachary B Smithline" [zachary.smithline_._yale.edu] Hi All,

(I'm so sorry this is so long!=C2=A0 Thank you so much, in advance!)
I have been having serious issues optimizing and trying to run a 2D scan along two bond lengths
for a ~200 atom protein active site, containing multiple Mg(II) atoms that<= br> have octahedral
coordination in Gaussian 16.=C2=A0 After relaxing the Hs at the AM1 level (holding everything else fixed),
I relaxed all atoms in my system, holding only the backbone fixed. I
noticed at this point that the
octahedral coordination geometries of all Mg(II) atoms were distorted.

Next, I started my relaxed scan along two bonds.=C2=A0 However, every time = I try
the scan, Gaussian
crashes and throws an error with the l103.exe.=C2=A0 Using opt=3Dcalcfc or = calcall
does not help.=C2=A0 Using
smaller step sizes (like 0.01 or 0.05 A as opposed to 0.1) simply delays the inevitable crash.

I have also tried repeating every step listed above using ONIOM B3LYP
6-31G(d)/AM1 where the
Mg(II) and neighboring atoms are treated with DFT and everything else is treated with AM1.=C2=A0 I still
got the same error.=C2=A0 This method is also too expensive and will not le= t me
get the whole scan!

***

MY QUESTIONS:

1. As a last ditch effort, I am trying to read in external AM1 parameters for Mg(II) (from this paper:
J. Chem. Theory Comput. 2006, 2, 1050-1056) that were designed to reproduce=
octahedral
coordination.=C2=A0 Am1=3DMOPACExternal didn't work, so I want to use a= m1=3Dinput
and read them in in
Gaussian syntax. I have listed the external parameters from the paper below=
(in MOPAC syntax)
and have also listed how I converted these parameters to Gaussian syntax. I have listed
everything in Gaussian syntax except the HSP and GSP parameters because I don't understand
the directions for how to write these in Gaussian syntax on the Gaussian info site.=C2=A0 Does anybody
know how to list HSP and GSP in Gaussian syntax?

Here is what my parameter file that I link to in my Gaussian input has (HSP=
and GSP I haven't
added yet):

Method=3D8 CoreType=3D1
****
Mg
U=3D12.83615,9.51125
Beta=3D1.26808,0.93230
ZetaOverlap=3D1.57114,1.25833
DCore=3D1.80310,1.99069,3.80477,0.66033,-0.00626,3.06817,1.
53666,-0.00581,2.33455,2.42691

Here are all the parameters I want to read in, in MOPAC format (reading it<= br> in this way didn't work):

USS=C2=A0 =C2=A0Mg=C2=A0 =C2=A012.83615
UPP=C2=A0 =C2=A0 Mg=C2=A0 =C2=A09.51125
BETAS=C2=A0 Mg=C2=A0 =C2=A01.26808
BETAP=C2=A0 Mg=C2=A0 =C2=A00.93230
ZS=C2=A0 =C2=A0 =C2=A0Mg=C2=A0 =C2=A0 1.57114
ZP=C2=A0 =C2=A0 =C2=A0Mg=C2=A0 =C2=A0 1.25833
ALP=C2=A0 =C2=A0 Mg=C2=A0 =C2=A0 1.80310
FN11=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 1.99069
FN21=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 3.80477
FN31=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 0.66033
FN12=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 0.00626
FN22=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 3.06817
FN32=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 1.53666
FN13=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 0.00581
FN23=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 2.33455
FN33=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 2.42691
GSP=C2=A0 =C2=A0 Mg=C2=A0 =C2=A0 8.29115
HSP=C2=A0 =C2=A0 Mg=C2=A0 =C2=A0 0.53547



2. Do you have any other advice for my issue with the l103.exe error?
Basically, I am trying to get
a large 2D PE surface for my system at the AM1 level. Once I have this, I will refine the
geometries/energies at each point on my surface in parallel at the DFT
level at some national
supercomputer.

***

If anybody knows how to help, please contact me at zachary.smithline^-^
yale.edu

Many thanks,
Zachary Smithline
Lab of Thomas Steitz
Depts. of MB&B and Chemistry
Yale Universityhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chem= istry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--001a114e5fec44f33e055= 74e340b
Content-Type: text/html; charset=3D"UTF-8"
Content-Transfer-Encoding: quoted-printable

<div dir=3D3D"auto">Is there such a thing as a .wfn to .wfx= converter, so tha=3D
t I can use Firefly output as input for Aimall, when ECPs are used?</div= ><d=3D
iv class=3D3D"gmail_extra"><br><div class=3D3D"g= mail_quote">On Aug 21, 2017 5:5=3D
8 PM, &quot;Zachary B Smithline zachary.smithline^^^<a href=3D3D&quo= t;http://yale= .=3D
edu">yale.edu</a>&quot; &lt;<a href=3D3D"mailto:owner-chemistry[*]ccl.net&qu= ot;>owne=3D
r-chemistry[*]ccl.net</a>&gt; wrote:<br type=3D3D"attribution&qu= ot;><blockquote clas=3D
s=3D3D"quote" style=3D3D"margin:0 0 0 .8ex;border-left:1px #= ccc solid;padding-l=3D
eft:1ex"><br>
Sent to CCL by: &quot;Zachary B Smithline&quot; [zachary.smithline_= ._<a hre=3D
f=3D3D"http://yale.edu" rel=3D3D"noreferrer" target=3D3D"= ;_blank">yale.edu</a>]<br=3D
>
Hi All,<br>
<br>
(I&#39;m so sorry this is so long!=3DC2=3DA0 Thank you so much, in adva= nce!)<br=3D
>
<br>
I have been having serious issues optimizing and trying to run a 2D scan al= =3D
ong two bond lengths<br>
for a ~200 atom protein active site, containing multiple Mg(II) atoms that = =3D
have octahedral<br>
coordination in Gaussian 16.=3DC2=3DA0 After relaxing the Hs at the AM1 lev= el (=3D
holding everything else fixed),<br>
I relaxed all atoms in my system, holding only the backbone fixed. I notice= =3D
d at this point that the<br>
octahedral coordination geometries of all Mg(II) atoms were distorted.<b= r>
<br>
Next, I started my relaxed scan along two bonds.=3DC2=3DA0 However, every t= ime =3D
I try the scan, Gaussian<br>
crashes and throws an error with the l103.exe.=3DC2=3DA0 Using opt=3D3Dcalc= fc or =3D
calcall does not help.=3DC2=3DA0 Using<br>
smaller step sizes (like 0.01 or 0.05 A as opposed to 0.1) simply delays th= =3D
e inevitable crash.<br>
<br>
I have also tried repeating every step listed above using ONIOM B3LYP 6-31G= =3D
(d)/AM1 where the<br>
Mg(II) and neighboring atoms are treated with DFT and everything else is tr= =3D
eated with AM1.=3DC2=3DA0 I still<br>
got the same error.=3DC2=3DA0 This method is also too expensive and will no= t le=3D
t me get the whole scan!<br>
<br>
***<br>
<br>
MY QUESTIONS:<br>
<br>
1. As a last ditch effort, I am trying to read in external AM1 parameters f= =3D
or Mg(II) (from this paper:<br>
J. Chem. Theory Comput. 2006, 2, 1050-1056) that were designed to reproduce= =3D
=C2=A0octahedral<br>
coordination.=3DC2=3DA0 Am1=3D3DMOPACExternal didn&#39;t work, so I wan= t to use a=3D
m1=3D3Dinput and read them in in<br>
Gaussian syntax. I have listed the external parameters from the paper below= =3D
=C2=A0(in MOPAC syntax)<br>
and have also listed how I converted these parameters to Gaussian syntax.= =3D
=3DC2=3DA0 I have listed<br>
everything in Gaussian syntax except the HSP and GSP parameters because I d= =3D
on&#39;t understand<br>
the directions for how to write these in Gaussian syntax on the Gaussian in= =3D
fo site.=3DC2=3DA0 Does anybody<br>
know how to list HSP and GSP in Gaussian syntax?<br>
<br>
Here is what my parameter file that I link to in my Gaussian input has (HSP= =3D
=C2=A0and GSP I haven&#39;t<br>
added yet):<br>
<br>
Method=3D3D8 CoreType=3D3D1<br>
****<br>
Mg<br>
U=3D3D12.83615,9.51125<br>
Beta=3D3D1.26808,0.93230<br>
ZetaOverlap=3D3D1.57114,1.25833<br>
DCore=3D3D1.80310,1.99069,3.80477,<wbr>0.66033,-0.00626,3.06817,1.<= ;wbr>53666,=3D
-0.00581,2.33455,2.42691<br>
<br>
Here are all the parameters I want to read in, in MOPAC format (reading it = =3D
in this way didn&#39;t work):<br>
<br>
USS=3DC2=3DA0 =3DC2=3DA0Mg=3DC2=3DA0 =3DC2=3DA012.83615<br>
UPP=3DC2=3DA0 =3DC2=3DA0 Mg=3DC2=3DA0 =3DC2=3DA09.51125<br>
BETAS=3DC2=3DA0 Mg=3DC2=3DA0 =3DC2=3DA01.26808<br>
BETAP=3DC2=3DA0 Mg=3DC2=3DA0 =3DC2=3DA00.93230<br>
ZS=3DC2=3DA0 =3DC2=3DA0 =3DC2=3DA0Mg=3DC2=3DA0 =3DC2=3DA0 1.57114<br>=
ZP=3DC2=3DA0 =3DC2=3DA0 =3DC2=3DA0Mg=3DC2=3DA0 =3DC2=3DA0 1.25833<br>=
ALP=3DC2=3DA0 =3DC2=3DA0 Mg=3DC2=3DA0 =3DC2=3DA0 1.80310<br>
FN11=3DC2=3DA0 =3DC2=3DA0Mg=3DC2=3DA0 =3DC2=3DA0 1.99069<br>
FN21=3DC2=3DA0 =3DC2=3DA0Mg=3DC2=3DA0 =3DC2=3DA0 3.80477<br>
FN31=3DC2=3DA0 =3DC2=3DA0Mg=3DC2=3DA0 =3DC2=3DA0 0.66033<br>
FN12=3DC2=3DA0 =3DC2=3DA0Mg=3DC2=3DA0 =3DC2=3DA0 0.00626<br>
FN22=3DC2=3DA0 =3DC2=3DA0Mg=3DC2=3DA0 =3DC2=3DA0 3.06817<br>
FN32=3DC2=3DA0 =3DC2=3DA0Mg=3DC2=3DA0 =3DC2=3DA0 1.53666<br>
FN13=3DC2=3DA0 =3DC2=3DA0Mg=3DC2=3DA0 =3DC2=3DA0 0.00581<br>
FN23=3DC2=3DA0 =3DC2=3DA0Mg=3DC2=3DA0 =3DC2=3DA0 2.33455<br>
FN33=3DC2=3DA0 =3DC2=3DA0Mg=3DC2=3DA0 =3DC2=3DA0 2.42691<br>
GSP=3DC2=3DA0 =3DC2=3DA0 Mg=3DC2=3DA0 =3DC2=3DA0 8.29115<br>
HSP=3DC2=3DA0 =3DC2=3DA0 Mg=3DC2=3DA0 =3DC2=3DA0 0.53547<br>
<br>
<br>
<br>
2. Do you have any other advice for my issue with the l103.exe error?=3DC2= =3DA0=3D
=C2=A0Basically, I am trying to get<br>
a large 2D PE surface for my system at the AM1 level. Once I have this, I w= =3D
ill refine the<br>
geometries/energies at each point on my surface in parallel at the DFT leve= =3D
l at some national<br>
supercomputer.<br>
<br>
***<br>
<br>
If anybody knows how to help, please contact me at zachary.smithline^-^<= a h=3D
ref=3D3D"http://yale.edu" rel=3D3D"noreferrer" target=3D3D&qu= ot;_blank">yale.edu</a><b=3D
r>
<br>
Many thanks,<br>
Zachary Smithline<br>
Lab of Thomas Steitz<br>
Depts. of MB&amp;B and Chemistry<br>
Yale University<br>
<br>
<br>
<br>
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--94eb2c1cde9a2689aa0557592cdf-- From owner-chemistry@ccl.net Tue Aug 22 16:02:00 2017 From: "Guzman, Francisco fg58-x-njit.edu" To: CCL Subject: CCL:G: l103.exe error and reading in external AM1 parameters Message-Id: <-52946-170822115633-17969-ZHHJcmgC3+9rAcbpENCHvg,,server.ccl.net> X-Original-From: "Guzman, Francisco" Content-Type: multipart/alternative; boundary="001a1147ffb442e9ab055759a355" Date: Tue, 22 Aug 2017 11:56:25 -0400 MIME-Version: 1.0 Sent to CCL by: "Guzman, Francisco" [fg58_._njit.edu] --001a1147ffb442e9ab055759a355 Content-Type: text/plain; charset="UTF-8" You can also try adding a dummy atom to avoid any linear angles. Linear angles cause the internal z-matrix conversions to crash. If you have a check file, you can also try restarting the optimization from here and add: geom=(checkpoint,newdefinition) to your route section. This is makes Gaussian re-define the internal coordinates for you. Sometimes this works, sometimes it doesn't. On Tue, Aug 22, 2017 at 1:06 AM, Norrby, Per-Ola Per-Ola.Norrby[] astrazeneca.com wrote: > > Sent to CCL by: "Norrby, Per-Ola" [Per-Ola.Norrby..astrazeneca.com] > Dear Zachary, > > You're trying to fix the wave function, but I believe an l103 error is > rather connected to a problem with the geometry definition. For geometry > optimization, Gaussian represents your molecule by a number of bonds, > angles, and torsions. If, during geometry optimization, an angle goes from > nonlinear to linear, this causes some torsions to become undefined, causing > a crash, fairly common. You might be able to simply restart from the point > of the crash, in which case Gaussian might recognize the linear bend and > set coordinates appropriately. However, I recommend trying to understand > your coordinates and take control if them with "ModRedundant". > > Best regards, > > Per-Ola > > Sent from my iPhone > > > On 22 Aug 2017, at 00:04, Zachary B Smithline zachary.smithline^^^ > yale.edu wrote: > > > > > > Sent to CCL by: "Zachary B Smithline" [zachary.smithline_._yale.edu] > > Hi All, > > > > (I'm so sorry this is so long! Thank you so much, in advance!) > > > > I have been having serious issues optimizing and trying to run a 2D scan > along two bond lengths > > for a ~200 atom protein active site, containing multiple Mg(II) atoms > that have octahedral > > coordination in Gaussian 16. After relaxing the Hs at the AM1 level > (holding everything else fixed), > > I relaxed all atoms in my system, holding only the backbone fixed. I > noticed at this point that the > > octahedral coordination geometries of all Mg(II) atoms were distorted. > > > > Next, I started my relaxed scan along two bonds. However, every time I > try the scan, Gaussian > > crashes and throws an error with the l103.exe. Using opt=calcfc or > calcall does not help. Using > > smaller step sizes (like 0.01 or 0.05 A as opposed to 0.1) simply delays > the inevitable crash. > > > > I have also tried repeating every step listed above using ONIOM B3LYP > 6-31G(d)/AM1 where the > > Mg(II) and neighboring atoms are treated with DFT and everything else is > treated with AM1. I still > > got the same error. This method is also too expensive and will not let > me get the whole scan! > > > > *** > > > > MY QUESTIONS: > > > > 1. As a last ditch effort, I am trying to read in external AM1 > parameters for Mg(II) (from this paper: > > J. Chem. Theory Comput. 2006, 2, 1050-1056) that were designed to > reproduce octahedral > > coordination. Am1=MOPACExternal didn't work, so I want to use am1=input > and read them in in > > Gaussian syntax. I have listed the external parameters from the paper > below (in MOPAC syntax) > > and have also listed how I converted these parameters to Gaussian > syntax. I have listed > > everything in Gaussian syntax except the HSP and GSP parameters because > I don't understand > > the directions for how to write these in Gaussian syntax on the Gaussian > info site. Does anybody > > know how to list HSP and GSP in Gaussian syntax? > > > > Here is what my parameter file that I link to in my Gaussian input has > (HSP and GSP I haven't > > added yet): > > > > Method=8 CoreType=1 > > **** > > Mg > > U=12.83615,9.51125 > > Beta=1.26808,0.93230 > > ZetaOverlap=1.57114,1.25833 > > DCore=1.80310,1.99069,3.80477,0.66033,-0.00626,3.06817,1. > 53666,-0.00581,2.33455,2.42691 > > > > Here are all the parameters I want to read in, in MOPAC format (reading > it in this way didn't work): > > > > USS Mg 12.83615 > > UPP Mg 9.51125 > > BETAS Mg 1.26808 > > BETAP Mg 0.93230 > > ZS Mg 1.57114 > > ZP Mg 1.25833 > > ALP Mg 1.80310 > > FN11 Mg 1.99069 > > FN21 Mg 3.80477 > > FN31 Mg 0.66033 > > FN12 Mg 0.00626 > > FN22 Mg 3.06817 > > FN32 Mg 1.53666 > > FN13 Mg 0.00581 > > FN23 Mg 2.33455 > > FN33 Mg 2.42691 > > GSP Mg 8.29115 > > HSP Mg 0.53547 > > > > > > > > 2. Do you have any other advice for my issue with the l103.exe error? > Basically, I am trying to get > > a large 2D PE surface for my system at the AM1 level. Once I have this, > I will refine the > > geometries/energies at each point on my surface in parallel at the DFT > level at some national > > supercomputer. > > > > *** > > > > If anybody knows how to help, please contact me at zachary.smithline^-^ > yale.edu > > > > Many thanks, > > Zachary Smithline > > Lab of Thomas Steitz > > Depts. of MB&B and Chemistry > > Yale University> https://clicktime.symantec.com/a/1/ > UULPNIaluQR3HPPh8gcC8e-E2B-fz9PhOVgkYljadNk=?d=K2- > LTKvY0KdXSIsPiMDsz2uQBSsohCf2aiF4JQM5clmaYa-JMApqZxKElcU6mGAg_ > as7dYBZ4tT4chGnXJfAOHYvsJNsGNdsTvyYloY6JQUjRmLvHzRN55b7m2a5e > JcAZePOzB4TdsXSCkJ2nH3-t92ZZhqcw4om1jxc4jSXkk9SgnVqpPk2Dvpg9OV0- > c9hX8jPYKlrtUtRFwmwaApOk1NECLF4mQUeRS5gRLbVrGfyhDxRWPq- > FBt5ntLIFVXVqv5TocXpsHKpQrCYeh8jGHv6_dUeyOSRbG6rUCIZnJUYi5orNYzufut569X- > joq8FjwJS2nRZuOEh5l0feUAiyzsRtVFVt17Lv4zRBnBCvsMlUbpNLGyszgMbk6- > uPNfeXXHzd5conERnXXZCTHizav3c_RN9WFXQSwaflHPDw-OekUpeTndpPT2z4q6FkHpYH- > yMKREb4MvgkBffiqPri7kN-HPIjXyUajeT00%3D&u=http%3A%2F% > 2Fwww.ccl.net%2Fcgi-bin%2Fccl%2Fsend_ccl_message> > https://clicktime.symantec.com/a/1/UULPNIaluQR3HPPh8gcC8e-E2B- > fz9PhOVgkYljadNk=?d=K2-LTKvY0KdXSIsPiMDsz2uQBSsohCf2aiF4JQM5clmaYa- > JMApqZxKElcU6mGAg_as7dYBZ4tT4chGnXJfAOHYvsJNsGNd > sTvyYloY6JQUjRmLvHzRN55b7m2a5eJcAZePOzB4TdsXSCkJ2nH3- > t92ZZhqcw4om1jxc4jSXkk9SgnVqpPk2Dvpg9OV0-c9hX8jPYKlrtUtRFwmwaApOk1NECLF > 4mQUeRS5gRLbVrGfyhDxRWPq-! 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If you have received this message > in error, please notify us and remove it from your system and note that you > must not copy, distribute or take any action in reliance on it. Any > unauthorized use or disclosure of the contents of this message is not > permitted and may be unlawful.> > > -- Francisco Guzman PhD Candidate Otto H. York Department of Chemical, Biological and Pharmaceutical Engineering New Jersey Institute of Technology Email: fg58::njit.edu, guzman.research::gmail.com Cell: 347-806-3977 --001a1147ffb442e9ab055759a355 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
You can also try adding a dummy atom t= o avoid any linear angles. Linear angles cause the internal z-matrix conver= sions to crash.

If you have a check file, you can also try res= tarting the optimization from here and add:

geom=3D(checkpoint= ,newdefinition)

to your route section.

This is ma= kes Gaussian re-define the internal coordinates for you. Sometimes this wor= ks, sometimes it doesn't.

On Tue, Aug 22, 2017 at 1:06 AM, Norrby, Per-Ola Per-= Ola.Norrby[]astrazeneca.com <= owner-chemistry::ccl.net> wrote:

Sent to CCL by: "Norrby, Per-Ola" [Per-Ola.Norrby..astrazeneca.= com]
Dear Zachary,

You're trying to fix the wave function, but I believe an l103 error is = rather connected to a problem with the geometry definition. For geometry op= timization, Gaussian represents your molecule by a number of bonds, angles,= and torsions. If, during geometry optimization, an angle goes from nonline= ar to linear, this causes some torsions to become undefined, causing a cras= h, fairly common. You might be able to simply restart from the point of the= crash, in which case Gaussian might recognize the linear bend and set coor= dinates appropriately. However, I recommend trying to understand your coord= inates and take control if them with "ModRedundant".

Best regards,

Per-Ola

Sent from my iPhone

> On 22 Aug 2017, at 00:04, Zachary B Smithline zachary.smithline^^^yale.edu &= lt;owner-chemistry##ccl.net> wrote:
>
>
> Sent to CCL by: "Zachary B Smithline" [zachary.smithline_._<= a href=3D"http://yale.edu" rel=3D"noreferrer" target=3D"_blank">yale.edu]
> Hi All,
>
> (I'm so sorry this is so long!=C2=A0 Thank you so much, in advance= !)
>
> I have been having serious issues optimizing and trying to run a 2D sc= an along two bond lengths
> for a ~200 atom protein active site, containing multiple Mg(II) atoms = that have octahedral
> coordination in Gaussian 16.=C2=A0 After relaxing the Hs at the AM1 le= vel (holding everything else fixed),
> I relaxed all atoms in my system, holding only the backbone fixed. I n= oticed at this point that the
> octahedral coordination geometries of all Mg(II) atoms were distorted.=
>
> Next, I started my relaxed scan along two bonds.=C2=A0 However, every = time I try the scan, Gaussian
> crashes and throws an error with the l103.exe.=C2=A0 Using opt=3Dcalcf= c or calcall does not help.=C2=A0 Using
> smaller step sizes (like 0.01 or 0.05 A as opposed to 0.1) simply dela= ys the inevitable crash.
>
> I have also tried repeating every step listed above using ONIOM B3LYP = 6-31G(d)/AM1 where the
> Mg(II) and neighboring atoms are treated with DFT and everything else = is treated with AM1.=C2=A0 I still
> got the same error.=C2=A0 This method is also too expensive and will n= ot let me get the whole scan!
>
> ***
>
> MY QUESTIONS:
>
> 1. As a last ditch effort, I am trying to read in external AM1 paramet= ers for Mg(II) (from this paper:
> J. Chem. Theory Comput. 2006, 2, 1050-1056) that were designed to repr= oduce octahedral
> coordination.=C2=A0 Am1=3DMOPACExternal didn't work, so I want to = use am1=3Dinput and read them in in
> Gaussian syntax. I have listed the external parameters from the paper = below (in MOPAC syntax)
> and have also listed how I converted these parameters to Gaussian synt= ax.=C2=A0 I have listed
> everything in Gaussian syntax except the HSP and GSP parameters becaus= e I don't understand
> the directions for how to write these in Gaussian syntax on the Gaussi= an info site.=C2=A0 Does anybody
> know how to list HSP and GSP in Gaussian syntax?
>
> Here is what my parameter file that I link to in my Gaussian input has= (HSP and GSP I haven't
> added yet):
>
> Method=3D8 CoreType=3D1
> ****
> Mg
> U=3D12.83615,9.51125
> Beta=3D1.26808,0.93230
> ZetaOverlap=3D1.57114,1.25833
> DCore=3D1.80310,1.99069,3.80477,0.66033,-0.00626,3.06817,1.5= 3666,-0.00581,2.33455,2.42691
>
> Here are all the parameters I want to read in, in MOPAC format (readin= g it in this way didn't work):
>
> USS=C2=A0 =C2=A0Mg=C2=A0 =C2=A012.83615
> UPP=C2=A0 =C2=A0 Mg=C2=A0 =C2=A09.51125
> BETAS=C2=A0 Mg=C2=A0 =C2=A01.26808
> BETAP=C2=A0 Mg=C2=A0 =C2=A00.93230
> ZS=C2=A0 =C2=A0 =C2=A0Mg=C2=A0 =C2=A0 1.57114
> ZP=C2=A0 =C2=A0 =C2=A0Mg=C2=A0 =C2=A0 1.25833
> ALP=C2=A0 =C2=A0 Mg=C2=A0 =C2=A0 1.80310
> FN11=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 1.99069
> FN21=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 3.80477
> FN31=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 0.66033
> FN12=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 0.00626
> FN22=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 3.06817
> FN32=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 1.53666
> FN13=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 0.00581
> FN23=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 2.33455
> FN33=C2=A0 =C2=A0Mg=C2=A0 =C2=A0 2.42691
> GSP=C2=A0 =C2=A0 Mg=C2=A0 =C2=A0 8.29115
> HSP=C2=A0 =C2=A0 Mg=C2=A0 =C2=A0 0.53547
>
>
>
> 2. Do you have any other advice for my issue with the l103.exe error?= =C2=A0 Basically, I am trying to get
> a large 2D PE surface for my system at the AM1 level. Once I have this= , I will refine the
> geometries/energies at each point on my surface in parallel at the DFT= level at some national
> supercomputer.
>
> ***
>
> If anybody knows how to help, please contact me at zachary.smithline^-= ^yale.edu<= /a>
>
> Many thanks,
> Zachary Smithline
> Lab of Thomas Steitz
> Depts. of MB&B and Chemistry
> Yale University>=C2=A0 =C2=A0 =C2=A0= https://clicktime.symantec.com/a/1/UULPNIaluQR3HPPh8gcC8e-E2B-fz9PhOVgkYljadNk=3D?d=3DK2-LTKvY0KdXSIsPiMDsz2uQBSsohCf2aiF4JQM= 5clmaYa-JMApqZxKElcU6mGAg_as7dYBZ4tT4chGnXJfAOHYvsJNsGNdsTvy= YloY6JQUjRmLvHzRN55b7m2a5eJcAZePOzB4TdsXSCkJ2nH3-t92ZZhqcw4om1jxc= 4jSXkk9SgnVqpPk2Dvpg9OV0-c9hX8jPYKlrtUtRFwmwaApOk1NECLF4mQUe= RS5gRLbVrGfyhDxRWPq-FBt5ntLIFVXVqv5TocXpsHKpQrCYeh8jGHv6_dUe= yOSRbG6rUCIZnJUYi5orNYzufut569X-joq8FjwJS2nRZuOEh5l0feUAiyzsRtVFVt17Lv4zRBnBCvsMlUbpNLGyszgMbk6-uPNfeXXHzd5conERnXXZCTHizav3c= _RN9WFXQSwaflHPDw-OekUpeTndpPT2z4q6FkHpYH-yMKREb4MvgkBffiqPr= i7kN-HPIjXyUajeT00%3D&u=3Dhttp%3A%2F%2Fwww.ccl.net%2Fcgi-bin%= 2Fccl%2Fsend_ccl_message>=C2=A0 =C2=A0 =C2=A0https://click= time.symantec.com/a/1/UULPNIaluQR3HPPh8gcC8e-E2B-fz9PhOVgkYl= jadNk=3D?d=3DK2-LTKvY0KdXSIsPiMDsz2uQBSsohCf2aiF4JQM5clmaYa-= JMApqZxKElcU6mGAg_as7dYBZ4tT4chGnXJfAOHYvsJNsGNdsTvyYloY6JQUjRmLv= HzRN55b7m2a5eJcAZePOzB4TdsXSCkJ2nH3-t92ZZhqcw4om1jxc4jSXkk9SgnVqp= Pk2Dvpg9OV0-c9hX8jPYKlrtUtRFwmwaApOk1NECLF4mQUeRS5gRLbVrGfyh= DxRWPq-!
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--001a1147ffb442e9ab055759a355-- From owner-chemistry@ccl.net Tue Aug 22 16:37:00 2017 From: "David Mannock dmannock]*[yahoo.com" To: CCL Subject: CCL:G: Vibrational sublevels along particular coordinate on PES Message-Id: <-52947-170822151903-23833-n1ywajIocoI99flmOSqqKw]-[server.ccl.net> X-Original-From: David Mannock Content-Type: multipart/alternative; boundary="----=_Part_3038229_1776586622.1503429284482" Date: Tue, 22 Aug 2017 19:14:44 +0000 (UTC) MIME-Version: 1.0 Sent to CCL by: David Mannock [dmannock===yahoo.com] ------=_Part_3038229_1776586622.1503429284482 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Wow! Gentlemen, 3 superb answers that I wish I'd had 5 years ago before ret= iring. You have given incredible insight into the issues involved that even= I can follow. Well explained and well thought out. David Mannock=20 On Monday, August 21, 2017 3:05 PM, Eric Hermes erichermes+/-gmail.com = wrote: =20 =20 Sent to CCL by: Eric Hermes [erichermes**gmail.com] On Sat, 2017-08-19 at 17:40 +0300, Igors Mihailovs igorsm**cfi.lu.lv wrote: > Dear Dr. Norrby, >=20 > Thank You for Your reply! But it seems to me that I might have been > right about that 'nonsence' in my question, because either I am > misinterpreting Your answer or You may have misinterpreted my > question. Or both :) >=20 > So I will describe my actual situation then. I have a discussion with > a synthetic chemist about interpreting the results of this PES scan. > There are actually two different scans, one in benzene and another > one in acetonitrile, with notably lower barrier in acetonitrile. One > of his arguments is that in acetonitrile there is larger population > of conformations with non-equilibrium dihedral=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0values (then it > might help to interpret some experimental findings about a certain > molecular electronic property). If calculated according to Boltzmann > distribution, some conformations with moderate deviations from the > equilibrium value of dihedral do have significant population with > respect to the equilibrium one (e.g., 0.2:1), because PES is > relatively flat in that region. If I do=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0unde= rstand correctly, in > reality only those conformations are really present in solution which > correspond to some vibrational sublevels on PES (or should it be > free-energy surface then?). I thought I could determine if a > conformation is something real if I plot vibrational sublevels in the > well and check whether a conformation is higher or lower than the > first of sublevels,=E2=80=A6 and so on. Is this the right idea at all? If= it > is, should these sublevels be taken from the calculations of > stationary points (well bottoms), or should I project those > sublevels, or =E2=80=A6? Because I cannot even found meaning of those > 'projected contributions' in my interpretation of how PES is related > to vibrational sublevels (above). So is this interpretation rather > wrong?=E2=80=A6 I am going to approach this problem from a statistical mechanical perspective. There is a correct way to do what you are doing, and I'll describe what that is, but it is important that you understand *why* that is the correct way. In order to discuss the population distribution of a system, we typically assume that the system's phase space can be broken up into individual "conformations" or "states", each of which occupies a well- defined region of the phase space. If we make this assumption, we can then assign a unique partition function (and corresponding free energy) to each of these regions (henceforth: states), which can then be used to investigate equilibrium properties of the system. The partition function of a system involves the configuration integral, which spans all of phase space (all possible atomic configurations). The partition function for a particular state is calculated by evaluating the configuration integral only over the region of phase space belonging to that state. Then, the relative probability of being in one of two states is given by the ratio of their partition functions. Practically speaking, these partition functions calculated through the use of several approximations (ideal gas, rigid rotor, harmonic oscillator...), rather than through explicit sampling of phase space. This is the approach that is typically used to calculate theoretical equilibrium constants. Note that carving up phase space into states in this way does not reduce the dimensionality of the configuration integral, it merely changes the limits of integration. Now, you are interested in the relative population of two points on a pre-defined 1-dimensional slice of the potential energy surface (PES), rather than the relative population of two regions of phase space.=C2=A0Thi= s means you can't calculate their relative population by taking the ratio of two 3N dimensional partition functions, because then the two regions of phase space that you are trying to compare will overlap. Instead, you must sample over a 3N-1 dimensional slice of phase space in which the coordinate along your 1 dimensional potential energy slice is held fixed. The approach is more or less the same as the approach I discussed previously, except you omit the direction corresponding to your reaction coordinate from the vibrational frequency analysis. As Per-Ola said, this can be done with Gaussian's freq=3Dprojected keyword. There are a few caveats: First, this approach may not be necessary at all! If the two points along your potential energy slice are sufficiently close to one another, then=C2=A0the remaining 3N-1 modes of th= e system may not differ much between the two points, meaning that the potential energy difference between those states will be a good approximation for the free energy difference. Second, this approach is only valid if your reaction coordinate is sufficiently flat that it can be treated classically. Otherwise, as Heribert mentions, the correct approach is to construct the vibrational wave function and evaluate its magnitude at each of the points you are interested in along the reaction coordinate.=20 As an aside, I would also like to make clear that this is related to (but distinct from) the elision of a degree of freedom when evaluating the free energy of a transition state within transition state theory. If the full 3Nx3N Hessian matrix of a transition state is diagonalized, one of the frequencies will be imaginary. The activation free energy is calculated by only considering the non-imaginary modes for the transition state, which reduces its dimensionality by 1. This is because rather than occupying a 3N dimensional region of phase space, the transition state is a 3N-1 dimensional dividing surface, which by definition has one fewer degree of freedom than the minima it connects. The transition state theory rate is k_B T/h * Q_TS/Q_R, where Q_TS is the partition function for the transition state and Q_R is the partition function for the reactants, and Q_TS has *one fewer dimension* than Q_R. However, since you want the relative population of two configurations on a 1-dimensional slice of the PES, BOTH of your partition functions will be 3N-1 dimensional. Eric Hermes >=20 > Thank You (and possibly others) again in advance. >=20 > Yours sincerely, > Igors Mihailovs > PhD student > ISSP University of Latvia >=20 >=20 > On 19/08/17 10:19, Norrby, Per-Ola Per-Ola.Norrby]|[astrazeneca.com > wrote: > > Dear Igors, > >=20 > > Adding vibrational contributions makes most sense at stationary > > points, you can use them when comparing stationary points, like the > > (fully converged) minima and transition state. If you need to, > > there is a way to calculate these contributions also at non- > > stationary points using Freq=3DProject in Gaussian. Note that you > > lose one degree of freedom, the direction of the force, which is > > projected out together with the translations and rotations (giving > > you N-7 degrees of freedom, not the usual N-6). > >=20 > > Per-Ola > >=20 > > Sent from my iPhone > >=20 > > On 18 Aug 2017, at 19:06, Igors Mihailovs igorsm=3D-=3Dcfi.lu.lv > > wrote: > >=20 > > > Dear computational chemistry specialists, > > >=20 > > > I have a question possibly of general knowledge (which I lack), > > > considering transfer of what I have learned about levels and > > > sublevels of diatomics to calculations of "big" molecules. > > > I am trying to analyze the potential energy surface of a > > > particular compound along one particular dihedral (by doing > > > partial optimizations at various values of this dihedral). This > > > cut of PES has double concave shape (like the small Greek > > > lambda), as if there were two potential wells separated by a > > > barrier (ca. 15 kcal/mol), corresponding to two conformers. If I > > > would be supposed to draw vibrational sublevels in both wells, > > > what would be their energies? The computed vibrational > > > frequencies (for stable structures at bottoms of both wells) with > > > respect to some line over the bottom? > > > The bottom should be the zero-point vibrational energy, but then > > > the one computed by Gaussian is about 70 times larger than the > > > barrier between two conformers (ca. 1015 kcal/mol). I suppose I > > > should take only contribution to ZPE from the dihedral in > > > interest to determine the first level in a well (since all the > > > modes are complex, do I need some diagonalization of something, > > > like to get "natural frequency modes"?). Is this so? If not, does > > > this result mean there is constant interconversion of both > > > conformers (sounds a bit ridiculous to me)? Or is this whole idea > > > of drawing vibration levels over such a cut in PES just a > > > nonsence? > > >=20 > > > Sorry for my illiteracy. And thanks in advance! > > >=20 > > > With best regards, > > > Igors Mihailovs > > > PhD student > > > ISSP University of Latvia > >=20 > > Confidentiality Notice: This message is private and may contain > > confidential and proprietary information. If you have received this > > message in error, please notify us and remove it from your system > > and note that you must not copy, distribute or take any action in > > reliance on it. Any unauthorized use or disclosure of the contents > > of this message is not permitted and may be unlawful. > =C2=A0 -=3D This is automatically added to each message by the mailing script =3D-=C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0Subscribe/Unsubscribe:=20 =C2=A0 =C2=A0 =C2=A0Job: http://www.ccl.net/jobs=20=C2=A0 =C2=A0 =C2=A0=20 ------=_Part_3038229_1776586622.1503429284482 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Wow! Gentlemen, 3 superb answers that I wish I'd had= 5 years ago before retiring. You have given incredible insight into the is= sues involved that even I can follow. Well explained and well thought out. = David Mannock


On Monday, August 21, 2017 3:05 PM, Eric Hermes erichermes+/-gmail.com &l= t;owner-chemistry---ccl.net> wrote:



Sent to CC= L by: Eric Hermes [erichermes**gmail.com]
On Sat,= 2017-08-19 at 17:40 +0300, Igors Mihailovs igorsm**cfi.lu.lv
wrote:
> Dear Dr. Norrby,
>
> Thank You for Your = reply! But it seems to me that I might have been
= > right about that 'nonsence' in my question, because either I am
> misinterpreting Your answer or You may have misint= erpreted my
> question. Or both :)
>
> So I will describe my a= ctual situation then. I have a discussion with
&g= t; a synthetic chemist about interpreting the results of this PES scan.
=
> There are actually two different scans, one in = benzene and another
> one in acetonitrile, wit= h notably lower barrier in acetonitrile. One
>= of his arguments is that in acetonitrile there is larger population
> of conformations with non-equilibrium dihedral&nbs= p;    values (then it
> mi= ght help to interpret some experimental findings about a certain
<= div dir=3D"ltr">> molecular electronic property). If calculated accordin= g to Boltzmann
> distribution, some conformati= ons with moderate deviations from the
> equili= brium value of dihedral do have significant population with
> respect to the equilibrium one (e.g., 0.2:1), because PES i= s
> relatively flat in that region. If I do&nb= sp;    understand correctly, in
> reality only those conformations are really present in solution whi= ch
> correspond to some vibrational sublevels = on PES (or should it be
> free-energy surface = then?). I thought I could determine if a
> con= formation is something real if I plot vibrational sublevels in the
> well and check whether a conformation is higher or l= ower than the
> first of sublevels,=E2=80=A6 a= nd so on. Is this the right idea at all? If it
&g= t; is, should these sublevels be taken from the calculations of
> stationary points (well bottoms), or should I project t= hose
> sublevels, or =E2=80=A6? Because I cann= ot even found meaning of those
> 'projected co= ntributions' in my interpretation of how PES is related
> to vibrational sublevels (above). So is this interpretation r= ather
> wrong?=E2=80=A6

I am going to approach this problem from a s= tatistical mechanical
perspective. There is a cor= rect way to do what you are doing, and I'll
descr= ibe what that is, but it is important that you understand *why*
that is the correct way.

In order to discuss the population distribution of a syst= em, we
typically assume that the system's phase s= pace can be broken up into
individual "conformati= ons" or "states", each of which occupies a well-
= defined region of the phase space. If we make this assumption, we can
then assign a unique partition function (and correspon= ding free energy)
to each of these regions (hence= forth: states), which can then be used
to investi= gate equilibrium properties of the system.

The partition function of a system involves the config= uration integral,
which spans all of phase space = (all possible atomic configurations).
The partiti= on function for a particular state is calculated by
evaluating the configuration integral only over the region of phase
<= /div>
space belonging to that state. Then, the relative pro= bability of being
in one of two states is given b= y the ratio of their partition
functions. Practic= ally speaking, these partition functions calculated
through the use of several approximations (ideal gas, rigid rotor,
harmonic oscillator...), rather than through explicit = sampling of phase
space. This is the approach tha= t is typically used to calculate
theoretical equi= librium constants. Note that carving up phase space
into states in this way does not reduce the dimensionality of the
configuration integral, it merely changes the limits of= integration.

Now, you= are interested in the relative population of two points on a
pre-defined 1-dimensional slice of the potential energy surfac= e (PES),
rather than the relative population of t= wo regions of phase space. This
means you ca= n't calculate their relative population by taking the ratio
of two 3N dimensional partition functions, because then the two = regions
of phase space that you are trying to com= pare will overlap. Instead,
you must sample over = a 3N-1 dimensional slice of phase space in which
= the coordinate along your 1 dimensional potential energy slice is held
<= /div>
fixed. The approach is more or less the same as the a= pproach I
discussed previously, except you omit t= he direction corresponding to
your reaction coord= inate from the vibrational frequency analysis. As
Per-Ola said, this can be done with Gaussian's freq=3Dprojected keyword.

There are a few caveats= : First, this approach may not be necessary at
al= l! If the two points along your potential energy slice are
sufficiently close to one another, then the remaining 3N-1 m= odes of the
system may not differ much between th= e two points, meaning that the
potential energy d= ifference between those states will be a good
app= roximation for the free energy difference. Second, this approach is
only valid if your reaction coordinate is sufficiently f= lat that it can
be treated classically. Otherwise= , as Heribert mentions, the correct
approach is t= o construct the vibrational wave function and evaluate its
magnitude at each of the points you are interested in along the
reaction coordinate.
As an aside, I would also like to make clear that = this is related to
(but distinct from) the elisio= n of a degree of freedom when evaluating
the free= energy of a transition state within transition state theory.
If the full 3Nx3N Hessian matrix of a transition state is diag= onalized,
one of the frequencies will be imaginar= y. The activation free energy is
calculated by on= ly considering the non-imaginary modes for the
tr= ansition state, which reduces its dimensionality by 1. This is
because rather than occupying a 3N dimensional region of phas= e space,
the transition state is a 3N-1 dimension= al dividing surface, which by
definition has one = fewer degree of freedom than the minima it connects.
The transition state theory rate is k_B T/h * Q_TS/Q_R, where Q_TS is
the partition function for the transition state an= d Q_R is the
partition function for the reactants= , and Q_TS has *one fewer
dimension* than Q_R. Ho= wever, since you want the relative population of
= two configurations on a 1-dimensional slice of the PES, BOTH of your
partition functions will be 3N-1 dimensional.
=

Eric Hermes

>
> Th= ank You (and possibly others) again in advance.
&= gt;
> Yours sincerely,
> Igors Mihailovs
> PhD student
> ISSP University of Latvia
>
>
> On 19= /08/17 10:19, Norrby, Per-Ola Per-Ola.Norrby]|[astrazeneca.com
> wrote:
> > Dear Igors,
> >
> > Add= ing vibrational contributions makes most sense at stationary
> > points, you can use them when comparing stationary po= ints, like the
> > (fully converged) minima= and transition state. If you need to,
> > = there is a way to calculate these contributions also at non-
> > stationary points using Freq=3DProject in Gaussian. N= ote that you
> > lose one degree of freedom= , the direction of the force, which is
> > = projected out together with the translations and rotations (giving
> > you N-7 degrees of freedom, not the usual N-6).=
> >
> > P= er-Ola
> >
> = > Sent from my iPhone
> >
> > On 18 Aug 2017, at 19:06, Igors Mihailovs igorsm=3D-= =3Dcfi.lu.lv
> > <owner-chemistry:-:ccl.= net> wrote:
> >
> > > Dear computational chemistry specialists,
> > >
> > > I have = a question possibly of general knowledge (which I lack),
> > > considering transfer of what I have learned about l= evels and
> > > sublevels of diatomics t= o calculations of "big" molecules.
> > >= I am trying to analyze the potential energy surface of a
> > > particular compound along one particular dihedral (= by doing
> > > partial optimizations at = various values of this dihedral). This
> > = > cut of PES has double concave shape (like the small Greek
> > > lambda), as if there were two potential wells = separated by a
> > > barrier (ca. 15 kca= l/mol), corresponding to two conformers. If I
>= ; > > would be supposed to draw vibrational sublevels in both wells,<= br>
> > > what would be their energies? The = computed vibrational
> > > frequencies (= for stable structures at bottoms of both wells) with
> > > respect to some line over the bottom?
> > > The bottom should be the zero-point vibrational ene= rgy, but then
> > > the one computed by = Gaussian is about 70 times larger than the
> &= gt; > barrier between two conformers (ca. 1015 kcal/mol). I suppose I
> > > should take only contribution to ZPE= from the dihedral in
> > > interest to = determine the first level in a well (since all the
> > > modes are complex, do I need some diagonalization of somet= hing,
> > > like to get "natural frequen= cy modes"?). Is this so? If not, does
> > &= gt; this result mean there is constant interconversion of both
> > > conformers (sounds a bit ridiculous to me)? Or= is this whole idea
> > > of drawing vib= ration levels over such a cut in PES just a
> = > > nonsence?
> > >
> > > Sorry for my illiteracy. And thanks in advance!=
> > >
> &= gt; > With best regards,
> > > Igors = Mihailovs
> > > PhD student
> > > ISSP University of Latvia
> >
> > Confidentiality Notice= : This message is private and may contain
> &g= t; confidential and proprietary information. If you have received this
<= /div>
> > message in error, please notify us and remo= ve it from your system
> > and note that yo= u must not copy, distribute or take any action in
> > reliance on it. Any unauthorized use or disclosure of the conten= ts
> > of this message is not permitted and= may be unlawful.
>  



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------=_Part_3038229_1776586622.1503429284482-- From owner-chemistry@ccl.net Tue Aug 22 17:12:00 2017 From: "Jim Kress jimkress35]^[gmail.com" To: CCL Subject: CCL:G: Wfn to wfx converter? Message-Id: <-52948-170822154254-29100-WHMdOwdiAMMuaDJQp+4Mzg=server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 22 Aug 2017 15:42:41 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [jimkress35[*]gmail.com] Firefly is not Gaussian and does not generate chk or fchk files. Jim Kress -----Original Message----- > From: owner-chemistry+jimkress35==gmail.com~~ccl.net [mailto:owner-chemistry+jimkress35==gmail.com~~ccl.net] On Behalf Of Víctor Luaña Cabal victor]=[fluor.quimica.uniovi.es Sent: Tuesday, August 22, 2017 10:48 AM To: Kress, Jim Subject: CCL:G: Wfn to wfx converter? Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor.:.fluor.quimica.uniovi.es] On Mon, Aug 21, 2017 at 09:17:59PM -0500, David Shobe shobedavid]![gmail.com wrote: > Is there such a thing as a .wfn to .wfx converter, so that I can use > Firefly output as input for Aimall, when ECPs are used? Maybe you can recover the results from the *.chk or *.fchk and ask gaussian to write the *.wfx. Not a wfn2wfx converter but it achieves the same. Regards, Dr. Víctor Luaña -- . . "Half of the US people use twitter to form its opinion and half / `' \ also elect the US president. I only hope they are not the same /(o)(o)\ half". --From a sentence by Gore Vidal /`. \/ .'\ / '`'` \ "[Technocrats, academics and journalists} are often motivated | \'`'`/ | by hope while the public at large tends to be more focused | |'`'`| | on fear." -- Russell Mead (The Washington Post, 2017) \/`'`'`'\/ ==(((==)))===================================+=========================== ! Dr.Víctor Luaña, in silico chemist & prof. ! ! Departamento de Química Física y Analítica ! ! Universidad de Oviedo, 33006-Oviedo, Spain ! ! e-mail: ! ! phone: +34-985-103491 fax: +34-985-103125 ! +--------------------------------------------+ GroupPage: Articles: git-hub: ORCID: 0000-0003-4585-4627; RID: H-2045-2015http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt