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

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_._ 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^-^ 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
>
>
>
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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" <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! 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 <div dir=3D"auto">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?</div><d= iv class=3D"gmail_extra"> <div class=3D"gmail_quote">On Aug 21, 2017 5:5= 8 PM, "Zachary B Smithline zachary.smithline^^^<a href=3D"http://yale.= edu">yale.edu</a>" <<a href=3D"mailto:owner-chemistry[*]ccl.net">owne= r-chemistry[*]ccl.net</a>> wrote: <blockquote 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_._<a hre= f=3D"http://yale.edu" rel=3D"noreferrer" target=3D"_blank">yale.edu</a>]<br=

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^-^<a h= ref=3D"http://yale.edu" rel=3D"noreferrer" target=3D"_blank">yale.edu</a><b= 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-= <br<br=<br E-mail to subscribers: <a href=3D"mailto:CHEMISTRY[*]ccl.net">CHEMISTRY[*]ccl.n= et</a> or use: =C2=A0 =C2=A0 =C2=A0 <a href=3D"http://www.ccl.net/cgi-bin/ccl/send_ccl_mes= sage" rel=3D"noreferrer" target=3D"_blank">http://www.ccl.net/cgi-bin/= ccl/send_ccl_message</a> E-mail to administrators: <a href=3D"mailto:CHEMISTRY-REQUEST[*]ccl.net">CHEM= ISTRY-REQUEST[*]ccl.net</a> or use =C2=A0 =C2=A0 =C2=A0 <a href=3D"http://www.ccl.net/cgi-bin/ccl/send_ccl_mes= sage" rel=3D"noreferrer" target=3D"_blank">http://www.ccl.net/cgi-bin/= ccl/send_ccl_message</a> Subscribe/Unsubscribe: =C2=A0 =C2=A0 =C2=A0 <a href=3D"http://www.ccl.net/chemistry/sub_unsub.shtm= l" rel=3D"noreferrer" target=3D"_blank">http://www.ccl.net/chemistry/s= ub_unsub.shtml</a> Before posting, check wait time at: <a href=3D"http://www.ccl.net" rel=3D"n= oreferrer" target=3D"_blank">http://www.ccl.net</a> Job: <a href=3D"http://www.ccl.net/jobs" rel=3D"noreferrer" target=3D"_blan= k">http://www.ccl.net/jobs</a> Conferences: <a href=3D"http://server.ccl.net/chemistry/announcements/confe= rences/" rel=3D"noreferrer" target=3D"_blank">http://server.ccl.net/ch= emistry/announcements/conferences/</a> Search Messages: <a href=3D"http://www.ccl.net/chemistry/searchccl/index.sh= tml" rel=3D"noreferrer" target=3D"_blank">http://www.ccl.net/chemistry/<wbr=

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-- С уважением, Тимур Маджидов Best regards, Timur Madzhidov ************************************************************************************************************** Senior Researcher, Assistant Professor, Responsible in charge of Master Program in Chemoinformatics Laboratory of Chemoinformatics and Molecular Modeling (http://cimm.kpfu.ru) Kazan Federal University, A.M. Butlerov Institute of Chemistry, Department of Organic Chemistry Казанский (Приволжский) федеральный университет, Химический институт им. А.М. Бутлерова, кафедра органической химии E-mail: Timur.Madzhidov|kpfu.ru, tmadzhidov|gmail.com Web-page: http://kpfu.ru/Timur.Madzhidov **************************************************************************************************************