From owner-chemistry@ccl.net Wed Oct 10 03:09:01 2007 From: "Stan van Gisbergen vangisbergen__scm.com" To: CCL Subject: CCL: About TAPE21 file (ADF program) Message-Id: <-35357-071009085750-17382-WHMdOwdiAMMuaDJQp+4Mzg/./server.ccl.net> X-Original-From: Stan van Gisbergen Content-Type: multipart/alternative; boundary=Apple-Mail-634-1026559851 Date: Tue, 9 Oct 2007 14:57:20 +0200 Mime-Version: 1.0 (Apple Message framework v752.3) Sent to CCL by: Stan van Gisbergen [vangisbergen+*+scm.com] --Apple-Mail-634-1026559851 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Dear Elizabeth, Please note that ADF questions are best directed to one of our online forums: http://www.scm.com/forums or to our support E-mail address: support at scm.com. One of my colleagues provided the following answer to your question: Answer: On TAPE21 these coefficients are stored in the section withe the name of the symmetry label of the orbital, and the variable name Eig-CoreSFO_A. (in an unrestricted calculation one has both Eig-CoreSFO_A and Eig- CoreSFO_B) Example: Suppose the symmetry of the orbitals is B1, then the command $ADFBIN/dmpkf filename.t21 "B1%Eig-CoreSFO_A" will print all these coefficients for all B1 orbitals. (Please note that the "pkf" utility gives you a table of contents of TAPE21.) Best regards, Stan van Gisbergen SCM On Oct 4, 2007, at 5:01 PM, Elizabeth Hernandez ehernand###ucalgary.ca wrote: > > Sent to CCL by: "Elizabeth Hernandez" [ehernand(-)ucalgary.ca] > Hi All, > > The output file (from ADF program) prints the MOs expanded in CFs > +SFOs, as in the following example: > > MOs expanded in CFs+SFOs > ======================== > > > MOs : 1 2 > occup: 2.00 0.00 > CF+SFO > 1 0.5489 1.2122 > 2 0.5489 -1.2122 > > > > Now, my questions are: > > Is it possible to find those coefficients somewhere in the > generated TAPE21 file? > > Or how to calculate them from the information stored in TAPE21? > > > Thanks, > > Elizabeth > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > > Dr. S.J.A. van Gisbergen Scientific Computing & Modelling NV Theoretical Chemistry, Vrije Universiteit De Boelelaan 1083 1081 HV Amsterdam The Netherlands vangisbergen : scm.com http://www.scm.com T: +31-20-5987626 F: +31-20-5987629 --Apple-Mail-634-1026559851 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 Dear Elizabeth,=A0

Please note that=A0ADF = questions are best directed to one of our online forums:=A0http://www.scm.com/forums

or to our support E-mail address: support at scm.com.=A0

One of my colleagues = provided the following answer to your question:=A0

On TAPE21 these coefficients are = stored in the section withe the name of the symmetry label of the = orbital,

and the variable name = Eig-CoreSFO_A.

(in an unrestricted calculation = one has both Eig-CoreSFO_A and Eig-CoreSFO_B)

Suppose the symmetry of the = orbitals is B1, then the command

$ADFBIN/dmpkf = filename.t21 "B1%Eig-CoreSFO_A"

will print = all these coefficients for all B1 orbitals.

(Please note that the "pkf" = utility gives you a table of contents of TAPE21.)

Best = regards,

Stan van Gisbergen

SCM=A0

On Oct 4, = 2007, at 5:01 PM, Elizabeth Hernandez ehernand###ucalgary.ca = wrote:

Sent to CCL by: "Elizabeth=A0 Hernandez" = [ehernand(-)ucalgary.ca]
Hi = All,

The output file (from ADF program) prints the MOs = expanded in CFs+SFOs, as in the following example:

MOs = expanded in CFs+SFOs

MOs = :=A0 =A0 =A0 1=A0 =A0 =A0 =A0 2
occup: =A0 = 2.00 =A0 =A0 = 0.00
CF+SFO
=A0=A0 =A0 = 1 =A0 0.5489 =A0 1.2122
=A0=A0 =A0 = 2 =A0 0.5489=A0 -1.2122

Now, my questions are:

Is it = possible to find those coefficients somewhere in the generated TAPE21 = file?

Or how to calculate them from the information stored = in TAPE21?=A0

Elizabeth

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Dr. S.J.A. van Gisbergen

Scientific Computing & Modelling NV

Theoretical Chemistry, Vrije Universiteit

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F: +31-20-5987629

Dear ccl users,

I would like to give a "computer aided drug design" course for the 5th year pharmacy students.

Any suggestions concerning the course, materials, software, lectures notes, ppt and others.

Fussy? Opinionated? Impossible to please? Perfect. Join Yahoo!'s user panel and lay it on us. --0-615025659-1192013811=:7918-- From owner-chemistry@ccl.net Wed Oct 10 11:19:00 2007 From: "John McKelvey jmmckel**gmail.com" To: CCL Subject: CCL: A Question About Z-Matrix and Mopac Inputs Message-Id: <-35360-071010104107-30177-XpARDww3LCHSxvCrIscM0g|,|server.ccl.net> X-Original-From: "John McKelvey" Content-Type: multipart/alternative; boundary="----=_Part_12920_5262087.1192023495105" Date: Wed, 10 Oct 2007 09:38:15 -0400 MIME-Version: 1.0 Sent to CCL by: "John McKelvey" [jmmckel[#]gmail.com] ------=_Part_12920_5262087.1192023495105 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline A picky point, but one can also specify "0SCF". This might be useful for really big systems where the 1SCF might take too much time. Cheers, John McKelvey On 10/9/07, Steve Bowlus chezbowlus]^[comcast.net wrote: > > > Sent to CCL by: Steve Bowlus [chezbowlus*comcast.net] > I don't know how newer or commercial versions of Mopac may have changed > this, > but for older versions (original 7)... > > For cartesian input, your options are only to freeze everything (_all_ > flags 0) > or optimize everything (all flags 1). > > You can get a mopac z-matrix by using the cartesian input and running 1SCF > (so > no geometry optimization occurs). Somewhere in the .out file there will > be a > z-matrix which can be edited into mopac input (.dat or .mop depending on > whose > version you use). As part of the editing process you can set the flags > for > individual distances/bond lengths, angles and dihedrals. In doing this be > certain that mopac has defined all of these coordinates in a sensible (for > your > purposes) fashion. For example, a distance between two arbitrary atoms > may be > used as a first coordinate (which may be chemical nonsense) while you > really > want a bond distance between specific atoms to be fixed. Also, depending > on > what you are fixing, you may be able to use mopac symmetry definitions to > speed > things up (I never do). > > If you are not satisfied with mopac's translation, you can always build > the > matrix by hand (**gasp!**). Once you become accustomed to doing so, this > is not > onerous for reasonably sized molecules, and well worth the effort for the > added > control over the calculation. Many other programs do the converson (e.g > Mol2Mol), but I can't say their translations will be superior to Mopac's. > > Cheers, > Steve > > Sina T reli sinatureli|gmail.com wrote: > > Sent to CCL by: "Sina T reli" [sinatureli-x-gmail.com] > > Hello, > > > > I want to run a calculation with mopac in which I need to freeze some > atoms. I was looking at the FAQ of mopac and it says in the z-matrix input > format there are two types of information, one of which is the atomic > coordinates which should supposedly be in the form: > > > > H -1.31 1 0.12 1 1.89 1 > > > > where if I change the 1's to 0's the atoms will be frozen. > > > > However the only information in the Z-matrix files are in the form of > > > > H 1.092 1 120.615 1 179.979 1 10 9 11 > > > > which state the bond distances, angles and dihedgral angles of the given > atom to other atoms. I tried to create both z-matrix and xyz files using > hyperchem and downloaded some samples from the website but none of them > seems to contain the atoms coordinate in the form given (xyz does contain > coordinates but then it is only a list of coordinates with nothing, no 0's > or 1's near the coordinates). > > > > How can I create mopac input files in which I can freeze atoms by the > form given above? > > > > Thanks alot...> > > > ------=_Part_12920_5262087.1192023495105 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline A picky point, but one can also specify "0SCF". This might be useful for really big systems where the 1SCF might take too much time.

Cheers,

John McKelvey

On 10/9/07, Steve Bowlus chezbowlus]^[comcast.net <owner-chemistry,,ccl.net> wrote:

Sent to CCL by: Steve Bowlus [chezbowlus*comcast.net]
I don't know how newer or commercial versions of Mopac may have changed this,
but for older versions (original 7)...

For cartesian input, your options are only to freeze everything (_all_ flags 0)
or optimize everything (all flags 1).

You can get a mopac z-matrix by using the cartesian input and running 1SCF (so
no geometry optimization occurs).  Somewhere in the .out file there will be a
z-matrix which can be edited into mopac input (.dat or .mop depending on whose
version you use).  As part of the editing process you can set the flags for
individual distances/bond lengths, angles and dihedrals.  In doing this be
certain that mopac has defined all of these coordinates in a sensible (for your
purposes) fashion.  For example, a distance between two arbitrary atoms may be
used as a first coordinate (which may be chemical nonsense) while you really
want a bond distance between specific atoms to be fixed.   Also, depending on
what you are fixing, you may be able to use mopac symmetry definitions to speed
things up (I never do).

If you are not satisfied with mopac's translation, you can always build the
matrix by hand (**gasp!**). Once you become accustomed to doing so, this is not
onerous for reasonably sized molecules, and well worth the effort for the added
control over the calculation.  Many other programs do the converson ( e.g
Mol2Mol), but I can't say their translations will be superior to Mopac's.

Cheers,
Steve

Sina T reli sinatureli|gmail.com wrote:
> Sent to CCL by: "Sina  T  reli" [ sinatureli-x-gmail.com]
> Hello,
>
> I want to run a calculation with mopac in which I need to freeze some atoms. I was looking at the FAQ of mopac and it says in the z-matrix input format there are two types of information, one of which is the atomic coordinates which should supposedly be in the form:
>
> H -1.31 1   0.12 1   1.89 1
>
> where if I change the 1's to 0's the atoms will be frozen.
>
> However the only information in the Z-matrix files are in the form of
>
> H 1.092   1 120.615   1 179.979  1 10 9 11
>
> which state the bond distances, angles and dihedgral angles of the given atom to other atoms. I tried to create both z-matrix and xyz files using hyperchem and downloaded some samples from the website but none of them seems to contain the atoms coordinate in the form given (xyz does contain coordinates but then it is only a list of coordinates with nothing, no 0's or 1's near the coordinates).
>
> How can I create mopac input files in which I can freeze atoms by the form given above?
>
> Thanks alot...>
>
>
>

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------=_Part_12920_5262087.1192023495105-- From owner-chemistry@ccl.net Wed Oct 10 12:26:00 2007 From: "Ivanciuc, Ovidiu I. oiivanci/a\utmb.edu" To: CCL Subject: CCL: A Question About Z-Matrix and Mopac Inputs Message-Id: <-35361-071010122320-28624-0Oua38rbQh4imOlDcufFfA{:}server.ccl.net> X-Original-From: "Ivanciuc, Ovidiu I." Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 10 Oct 2007 11:23:09 -0500 MIME-Version: 1.0 Sent to CCL by: "Ivanciuc, Ovidiu I." [oiivanci(0)utmb.edu] >>> I tried to create both z-matrix and xyz files using hyperchem and >>> downloaded some samples from the website but none of them seems >>> to contain the atoms coordinate in the form given >>>How can I create mopac input files in which I can freeze atoms by the = form given above? It is strange that the Hyperchem z-matrix filed don't contain the = optimization flag. Here you have a fragment of a file saved with Hyperchem 3, and as you = can see it has the flags set for optimization; to freeze a bond/angle/torsion = angle, just edit the file and replace "1" with "0" for that substructure: AM1 VECTORS BONDS PI POLAR PRECISE ENPART Cyclooxygenase inhibitor cox_001 C 00000.0000 0 00000.0000 0 00000.0000 0 0 0 0 C 00001.3949 1 00000.0000 0 00000.0000 0 1 0 0 C 00001.3940 1 00120.1946 1 00000.0000 0 2 1 0 C 00001.4013 1 00119.9210 1 00359.9167 1 3 2 1 C 00001.4021 1 00119.7847 1 00000.2039 1 4 3 2 C 00001.3935 1 00119.9198 1 00359.8241 1 5 4 3 C 00001.4527 1 00120.6513 1 00177.4582 1 4 3 2 N 00001.4207 1 00125.9946 1 00062.3579 1 7 4 3 N 00001.3409 1 00111.7044 1 00182.1369 1 8 7 4 A similar result might be obtained with OpenBabel, = http://openbabel.sourceforge.net/wiki/Main_Page (hin to mopin): C 0.000000 1 0.000000 1 0.000000 1 0 0 0 C 1.394925 1 0.000000 1 0.000000 1 1 0 0 C 1.394028 1 120.194680 1 0.000000 1 2 1 0 C 1.401340 1 119.921069 1 359.916798 1 3 2 1 C 1.402142 1 119.784720 1 0.203970 1 4 3 2 C 1.393528 1 119.919866 1 359.824141 1 5 4 3 C 1.452774 1 120.651399 1 177.458230 1 4 3 2 N 1.420735 1 125.994664 1 62.357957 1 7 4 3 N 1.340965 1 111.704436 1 182.136934 1 8 7 4 So, if your Hyperchem does not produce a proper z-matrix file, just use OpenBabel. O. From owner-chemistry@ccl.net Wed Oct 10 13:39:00 2007 From: "Ivanciuc, Ovidiu I. oiivanci+*+utmb.edu" To: CCL Subject: CCL: Drug design course Message-Id: <-35362-071010133336-26713-mftjc8BDWH/BhG7dMFkxZA]|[server.ccl.net> X-Original-From: "Ivanciuc, Ovidiu I." Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 10 Oct 2007 12:32:45 -0500 MIME-Version: 1.0 Sent to CCL by: "Ivanciuc, Ovidiu I." [oiivanci:utmb.edu] > I will appreciate any comments or suggestions concerning this course > including textbook, lecture notes, handouts, power point presentation, > excercises ...etc See Molecular Conceptor http://www.molecular-conceptor.com/home.html O. From owner-chemistry@ccl.net Wed Oct 10 14:51:01 2007 From: "Daniil Bratashov dn2010(-)gmail.com" To: CCL Subject: CCL: Ag:Si(111) Surface Message-Id: <-35363-071010144806-2457-Phas3tJNPJ0oTVm364yr1Q-$-server.ccl.net> X-Original-From: Daniil Bratashov Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII Date: Wed, 10 Oct 2007 21:08:07 +0400 Mime-Version: 1.0 Sent to CCL by: Daniil Bratashov [dn2010%a%gmail.com] On Tue, 9 Oct 2007 20:11:45 +0100 "CCL CCL computationalchemist-#-gmail.com" wrote: > Could any one please let me know, how a Ag:Si(111) surface look like. In microchip fabrication Si surface usually covered with thin amorphous SiO2 layer. SiO2 in usual semiconductor technology terminated with different variants of -O-H clusters, hydrogen bonded H2O and so on. (Kiselev, Kozlov, Zoteev. Osnovy fiziki poverhnosti tvyordogo tela (MGU, 1999)(ru)(T)(294s)) With deposition of Ag most of H2O must be removed > from surface by heat, vacuum and so on and -O-H group to my mind can be converted to oxygen bridge Si-O-Me or something like it. I'm not sure, that this model is complete and accurate, It's all, that I can remember from lectures on physical chemistry of semiconductor surface. WBR, Daniil Bratashov. From owner-chemistry@ccl.net Wed Oct 10 15:28:01 2007 From: "=?ISO-8859-1?Q?Sina_T=FCreli?= sinatureli^_^gmail.com" To: CCL Subject: CCL: A Question About Z-Matrix and Mopac Inputs Message-Id: <-35364-071010121645-27976-3s7dA6s3iGvgVW68U3wihw##server.ccl.net> X-Original-From: "=?ISO-8859-1?Q?Sina_T=FCreli?=" Content-Type: multipart/alternative; boundary="----=_Part_16656_23744043.1192032926950" Date: Wed, 10 Oct 2007 19:15:26 +0300 MIME-Version: 1.0 Sent to CCL by: "=?ISO-8859-1?Q?Sina_T=FCreli?=" [sinatureli-,-gmail.com] ------=_Part_16656_23744043.1192032926950 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Well I just found the keyword that converts the connectivity input into others such as the cartesian coordinates input. In which near each coordinate of each atom is +1 (except for the center atom which is kept fixed), +1 meaning it can be moved. So you can actually just change atoms you want to be kept fixed to 0+. My system is rather large with about 400-500 atoms building by hand would indeed be *gasp*. I also use a text editor to change all the +1s to +0 and change back the few (about 50) atoms I want to optimize back to +1. I was indeed using 0SCF to convert the format not because I knew it was faster, but because I am new to mopac and dont really know the other keywords :p I think I am going to start coding a perl/tk gui application that can do such modifications (freezing atoms angles etc) and extend it into something more useful later (such as the gui that exists for mopac already). Manually changing 50 atoms back to +1 still manually changing 150 entries :p On 10/10/07, John McKelvey jmmckel**gmail.com wrote: > > A picky point, but one can also specify "0SCF". This might be useful for > really big systems where the 1SCF might take too much time. > > Cheers, > > John McKelvey > > On 10/9/07, Steve Bowlus chezbowlus]^[comcast.net < > owner-chemistry-#-ccl.net> wrote: > > > > > Sent to CCL by: Steve Bowlus [chezbowlus*comcast.net] > > I don't know how newer or commercial versions of Mopac may have changed > > this, > > but for older versions (original 7)... > > > > For cartesian input, your options are only to freeze everything (_all_ > > flags 0) > > or optimize everything (all flags 1). > > > > You can get a mopac z-matrix by using the cartesian input and running > > 1SCF (so > > no geometry optimization occurs). Somewhere in the .out file there will > > be a > > z-matrix which can be edited into mopac input (.dat or .mop depending on > > whose > > version you use). As part of the editing process you can set the flags > > for > > individual distances/bond lengths, angles and dihedrals. In doing this > > be > > certain that mopac has defined all of these coordinates in a sensible > > (for your > > purposes) fashion. For example, a distance between two arbitrary atoms > > may be > > used as a first coordinate (which may be chemical nonsense) while you > > really > > want a bond distance between specific atoms to be fixed. Also, > > depending on > > what you are fixing, you may be able to use mopac symmetry definitions > > to speed > > things up (I never do). > > > > If you are not satisfied with mopac's translation, you can always build > > the > > matrix by hand (**gasp!**). Once you become accustomed to doing so, this > > is not > > onerous for reasonably sized molecules, and well worth the effort for > > the added > > control over the calculation. Many other programs do the converson ( > > e.g > > Mol2Mol), but I can't say their translations will be superior to > > Mopac's. > > > > Cheers, > > Steve > > > > Sina T reli sinatureli|gmail.com wrote: > > > Sent to CCL by: "Sina T reli" [ sinatureli-x-gmail.com] > > > Hello, > > > > > > I want to run a calculation with mopac in which I need to freeze some > > atoms. I was looking at the FAQ of mopac and it says in the z-matrix input > > format there are two types of information, one of which is the atomic > > coordinates which should supposedly be in the form: > > > > > > H -1.31 1 0.12 1 1.89 1 > > > > > > where if I change the 1's to 0's the atoms will be frozen. > > > > > > However the only information in the Z-matrix files are in the form of > > > > > > H 1.092 1 120.615 1 179.979 1 10 9 11 > > > > > > which state the bond distances, angles and dihedgral angles of the > > given atom to other atoms. I tried to create both z-matrix and xyz files > > using hyperchem and downloaded some samples from the website but none of > > them seems to contain the atoms coordinate in the form given (xyz does > > contain coordinates but then it is only a list of coordinates with nothing, > > no 0's or 1's near the coordinates). > > > > > > How can I create mopac input files in which I can freeze atoms by the > > form given above? > > > > > > Thanks alot...> > > > > > > > > > > > > > > > > > > > E-mail to subscribers: CHEMISTRY-#-ccl.net or use:> > > > E-mail to administrators: CHEMISTRY-REQUEST-#-ccl.net or use> > > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > > search)> > > > > > > > > > > > > ------=_Part_16656_23744043.1192032926950 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline

Well I just found the keyword that converts the connectivity input into others such as the cartesian coordinates input. In which near each coordinate of each atom is +1 (except for the center atom which is kept fixed), +1 meaning it can be moved. So you can actually just change atoms you want to be kept fixed to 0+. My system is rather large with about 400-500 atoms building by hand would indeed be *gasp*. I also use a text editor to change all the +1s to +0 and change back the few (about 50) atoms I want to optimize back to +1.

I was indeed using 0SCF to convert the format not because I knew it was faster, but because I am new to mopac and dont really know the other keywords :p

I think I am going to start coding a perl/tk gui application that can do such modifications (freezing atoms angles etc) and extend it into something more useful later (such as the gui that exists for mopac already). Manually changing 50 atoms back to +1 still manually changing 150 entries :p

On 10/10/07, John McKelvey jmmckel**gmail.com <owner-chemistry{}ccl.net> wrote:

A picky point, but one can also specify "0SCF". This might be useful for really big systems where the 1SCF might take too much time.

Cheers,

John McKelvey

On 10/9/07, Steve Bowlus chezbowlus]^[ comcast.net <owner-chemistry-#-ccl.net> wrote:

Sent to CCL by: Steve Bowlus [chezbowlus*comcast.net]
I don't know how newer or commercial versions of Mopac may have changed this,
but for older versions (original 7)...

For cartesian input, your options are only to freeze everything (_all_ flags 0)
or optimize everything (all flags 1).

You can get a mopac z-matrix by using the cartesian input and running 1SCF (so
no geometry optimization occurs).  Somewhere in the .out file there will be a
z-matrix which can be edited into mopac input (.dat or .mop depending on whose
version you use).  As part of the editing process you can set the flags for
individual distances/bond lengths, angles and dihedrals.  In doing this be
certain that mopac has defined all of these coordinates in a sensible (for your
purposes) fashion.  For example, a distance between two arbitrary atoms may be
used as a first coordinate (which may be chemical nonsense) while you really
want a bond distance between specific atoms to be fixed.   Also, depending on
what you are fixing, you may be able to use mopac symmetry definitions to speed
things up (I never do).

If you are not satisfied with mopac's translation, you can always build the
matrix by hand (**gasp!**). Once you become accustomed to doing so, this is not
onerous for reasonably sized molecules, and well worth the effort for the added
control over the calculation.  Many other programs do the converson ( e.g
Mol2Mol), but I can't say their translations will be superior to Mopac's.

Cheers,
Steve

Sina T reli sinatureli|gmail.com wrote:
> Sent to CCL by: "Sina  T  reli" [ sinatureli-x-gmail.com]
> Hello,
>
> I want to run a calculation with mopac in which I need to freeze some atoms. I was looking at the FAQ of mopac and it says in the z-matrix input format there are two types of information, one of which is the atomic coordinates which should supposedly be in the form:
>
> H -1.31 1   0.12 1   1.89 1
>
> where if I change the 1's to 0's the atoms will be frozen.
>
> However the only information in the Z-matrix files are in the form of
>
> H 1.092   1 120.615   1 179.979  1 10 9 11
>
> which state the bond distances, angles and dihedgral angles of the given atom to other atoms. I tried to create both z-matrix and xyz files using hyperchem and downloaded some samples from the website but none of them seems to contain the atoms coordinate in the form given (xyz does contain coordinates but then it is only a list of coordinates with nothing, no 0's or 1's near the coordinates).
>
> How can I create mopac input files in which I can freeze atoms by the form given above?
>
> Thanks alot...>
>
>
>

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------=_Part_16656_23744043.1192032926950-- From owner-chemistry@ccl.net Wed Oct 10 17:53:00 2007 From: "Peter Nielsen peter^daylight.com" To: CCL Subject: CCL: computer aided drug design course Message-Id: <-35365-071010174715-19499-+Lk+K66HgDGt8834xYcRGw---server.ccl.net> X-Original-From: Peter Nielsen Content-type: multipart/alternative; boundary=Apple-Mail-28--1007363240 Date: Wed, 10 Oct 2007 16:30:01 -0400 MIME-version: 1.0 (Apple Message framework v752.2) Sent to CCL by: Peter Nielsen [peter!A!daylight.com] --Apple-Mail-28--1007363240 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Omar: The Daylight language tutorials may be appropriate. Let us know if you need any support. http://www.daylight.com/dayhtml_tutorials/index.html Thanks, Peter __________________________________________ Peter Nielsen Director, Marketing & Business Development DAYLIGHT CHEMICAL INFORMATION SYSTEMS, Inc. http://www.daylight.com tel: 802-223-9831 fax: 206-203-0961 mobile: 802-598-4819 On Oct 10, 2007, at 6:56 AM, omar Deeb deeb2000il[A]yahoo.com wrote: > Dear ccl users, > I would like to give a "computer aided drug design" course for the > 5th year pharmacy students. > Any suggestions concerning the course, materials, software, > lectures notes, ppt and others. > Thanks in advance > > Dr. Omar Deeb > Al-Quds University > Jerusalem > > Fussy? Opinionated? Impossible to please? Perfect. Join Yahoo!'s > user panel and lay it on us. --Apple-Mail-28--1007363240 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 Omar:

The Daylight language = tutorials may be appropriate.=A0 Let us know if you need any = support.

http://www.d= aylight.com/dayhtml_tutorials/index.html

Thanks,

Peter

__________________________________________

Peter Nielsen

Director, = Marketing & Business Development

DAYLIGHT = CHEMICAL INFORMATION SYSTEMS, Inc.

http://www.daylight.com

tel: 802-223-9831

fax: = 206-203-0961

mobile: = 802-598-4819

=A0

On = Oct 10, 2007, at 6:56 AM, omar Deeb deeb2000il[A]yahoo.com = wrote:

Dear ccl users,

I would like to give a = "computer aided drug design" course=A0for the 5th year pharmacy = students.

Any suggestions concerning the course, materials, = software, lectures notes, ppt and others.

Thanks in = advance

=A0

Dr. Omar Deeb

Al-Quds = University

Jerusalem=A0

Fussy? = Opinionated? Impossible to please? Perfect. Join Yahoo!'s user panel and lay = it on us.

= --Apple-Mail-28--1007363240-- From owner-chemistry@ccl.net Wed Oct 10 19:36:01 2007 From: "=?ISO-8859-1?Q?Sina_T=FCreli?= sinatureli=-=gmail.com" To: CCL Subject: CCL: A Question About Z-Matrix and Mopac Inputs Message-Id: <-35366-071010145447-4319-LT+Jd5m5kGSRrjTm0A0feg:server.ccl.net> X-Original-From: "=?ISO-8859-1?Q?Sina_T=FCreli?=" Content-Type: multipart/alternative; boundary="----=_Part_16932_4311246.1192042472274" Date: Wed, 10 Oct 2007 21:54:32 +0300 MIME-Version: 1.0 Sent to CCL by: "=?ISO-8859-1?Q?Sina_T=FCreli?=" [sinatureli^^gmail.com] ------=_Part_16932_4311246.1192042472274 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Z-Matrix has only connectivity though as in your case too. I can only freeze bond angles, dihedrales and specific bond lengths not coordinates. I found the way however, there is a key in mopac that converts z-matrix files into coordinate files for mopac. Thanks though On 10/10/07, Ivanciuc, Ovidiu I. oiivanci/autmb.edu wrote: > > > Sent to CCL by: "Ivanciuc, Ovidiu I." [oiivanci(0)utmb.edu] > > >>> I tried to create both z-matrix and xyz files using hyperchem and > >>> downloaded some samples from the website but none of them seems > >>> to contain the atoms coordinate in the form given > > >>>How can I create mopac input files in which I can freeze atoms by the > form given above? > > It is strange that the Hyperchem z-matrix filed don't contain the > optimization flag. > Here you have a fragment of a file saved with Hyperchem 3, and as you can > see > it has the flags set for optimization; to freeze a bond/angle/torsion > angle, > just edit the file and replace "1" with "0" for that substructure: > > AM1 VECTORS BONDS PI POLAR PRECISE ENPART > Cyclooxygenase inhibitor cox_001 > > C 00000.0000 0 00000.0000 0 00000.0000 0 0 0 0 > C 00001.3949 1 00000.0000 0 00000.0000 0 1 0 0 > C 00001.3940 1 00120.1946 1 00000.0000 0 2 1 0 > C 00001.4013 1 00119.9210 1 00359.9167 1 3 2 1 > C 00001.4021 1 00119.7847 1 00000.2039 1 4 3 2 > C 00001.3935 1 00119.9198 1 00359.8241 1 5 4 3 > C 00001.4527 1 00120.6513 1 00177.4582 1 4 3 2 > N 00001.4207 1 00125.9946 1 00062.3579 1 7 4 3 > N 00001.3409 1 00111.7044 1 00182.1369 1 8 7 4 > > A similar result might be obtained with OpenBabel, > http://openbabel.sourceforge.net/wiki/Main_Page > (hin to mopin): > > C 0.000000 1 0.000000 1 0.000000 1 0 0 0 > C 1.394925 1 0.000000 1 0.000000 1 1 0 0 > C 1.394028 1 120.194680 1 0.000000 1 2 1 0 > C 1.401340 1 119.921069 1 359.916798 1 3 2 1 > C 1.402142 1 119.784720 1 0.203970 1 4 3 2 > C 1.393528 1 119.919866 1 359.824141 1 5 4 3 > C 1.452774 1 120.651399 1 177.458230 1 4 3 2 > N 1.420735 1 125.994664 1 62.357957 1 7 4 3 > N 1.340965 1 111.704436 1 182.136934 1 8 7 4 > > So, if your Hyperchem does not produce a proper z-matrix file, just > use OpenBabel. > > O. > > > > - This is automatically added to each message by the mailing script -> > > > ------=_Part_16932_4311246.1192042472274 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Z-Matrix has only connectivity though as in your case too. I can only freeze bond angles, dihedrales and specific bond lengths not coordinates. I found the way however, there is a key in mopac that converts z-matrix files into coordinate files for mopac. Thanks though

On 10/10/07, Ivanciuc, Ovidiu I. oiivanci/autmb.edu <owner-chemistry^^^ccl.net> wrote:

Sent to CCL by: "Ivanciuc, Ovidiu I." [oiivanci(0)utmb.edu]

>>> I tried to create both z-matrix and xyz files using hyperchem and
>>> downloaded some samples from the website but none of them seems
>>> to contain the atoms coordinate in the form given

>>>How can I create mopac input files in which I can freeze atoms by the form given above?

It is strange that the Hyperchem z-matrix filed don't contain the optimization flag.
Here you have a fragment of a file saved with Hyperchem 3, and as you can see
it has the flags set for optimization; to freeze a bond/angle/torsion angle,
just edit the file and replace "1" with "0" for that substructure:

AM1 VECTORS BONDS PI POLAR PRECISE ENPART
Cyclooxygenase inhibitor cox_001

C     00000.0000 0  00000.0000 0  00000.0000 0 0 0 0
C     00001.3949 1  00000.0000 0  00000.0000 0 1 0 0
C     00001.3940 1  00120.1946 1  00000.0000 0 2 1 0
C     00001.4013 1  00119.9210 1  00359.9167 1 3 2 1
C     00001.4021 1  00119.7847 1  00000.2039 1 4 3 2
C     00001.3935 1  00119.9198 1  00359.8241 1 5 4 3
C     00001.4527 1  00120.6513 1  00177.4582 1 4 3 2
N     00001.4207 1  00125.9946 1  00062.3579 1 7 4 3
N     00001.3409 1  00111.7044 1  00182.1369 1 8 7 4

A similar result might be obtained with OpenBabel, http://openbabel.sourceforge.net/wiki/Main_Page
(hin to mopin):

C    0.000000  1    0.000000  1    0.000000  1     0   0   0
C    1.394925  1    0.000000  1    0.000000  1     1   0   0
C    1.394028  1   120.194680  1    0.000000  1     2   1   0
C    1.401340  1  119.921069  1  359.916798  1     3   2   1
C    1.402142  1  119.784720  1    0.203970  1     4   3   2
C    1.393528  1  119.919866  1  359.824141  1     5   4   3
C    1.452774  1  120.651399  1  177.458230  1     4   3   2
N    1.420735  1  125.994664  1   62.357957  1     7   4   3
N    1.340965  1  111.704436  1  182.136934  1     8   7   4

So, if your Hyperchem does not produce a proper z-matrix file, just
use OpenBabel.

O.

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------=_Part_16932_4311246.1192042472274-- From owner-chemistry@ccl.net Wed Oct 10 20:53:00 2007 From: "Sengen Sun sengensun _ yahoo.com" To: CCL Subject: CCL: Q & A: history and reality Message-Id: <-35367-071010205002-24829-01b+x5BRaySQ7yp4JvqauA..server.ccl.net> X-Original-From: Sengen Sun Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Wed, 10 Oct 2007 17:49:51 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Sengen Sun [sengensun%%yahoo.com] Question: > Dear Sengen, > > I have a question with your comment. It is > common practice that organic chemists > draw the electron flow arrows from an > electron-rich center to an electron- > deficient center, which is essentially > the same as that electrons flow toward > positive potential. > Is anything wrong with that? > ......... ...... --------------------------------- Answer: At least a century ago (or two?), organic chemists started to explain mechanisms based on charge distribution in reactants, which is equivalent to the electrostatic potential argument. Organic chemists could correctly draw the arrows for the reactions such as that between fulminic acid and ethyne a century ago (!!!), based on the empirical knowledge that electron-rich oxygen donates and electron-deficient carbon of fulminic acid accepts electron. They could until they could not. . At least, chemists became completely confused by the regioselectivity of 1,3-dipolar cycloadditions, which are a huge class of reactions in practical syntheses of heterocycles (Christl & Huisgen: Tetrahedron Lett 1968, 5209). The regioselectivity made chemists confused with some reactions (such as that between fulminic acid and ethyne) that could have been well understood a century ago. In my personal view, Huisgen (maybe Christl also) should have been awarded a Nobel prize for the pioneer experimental work, which not only fascinated me for the last 27 years since I was an under, but also has induced the unprecedented hot debates in the literature for about 4 decades on mechanisms. The regioselectivity demonstrates us how the nature can trick us by hiding the dynamic events > from the state properties within the well-established physical laws. . The regioselectivity is one of the few reasons that the highest authority in theoretical chemistry attempts to abolish the meaning of arrows for this whole class of concerted cycloadditions, for which they used a special word "non-classical". . A book of Modern Physical Organic Chemistry (by E.V. Anslyn & D. A. Doughenty, Ed. 2006, page 894) says "The mechanisms are best described by the orbital and state correlation diagrams... The electron pushing does not reflect how the reaction actually occurs". This is just a recent example of many in the literature that orbital control theories deny electrostatic forces or the effect of electrostatic potential. They don't mention the electrostatic forces (or polar effect) until orbitals fail in prediction. On the other hand, there have been strongly inquiring minds in the literature for the recent decade who attempt to re-establish the meaning of the arrows in cycloadditions, but have led to the controversies what is the correct direction for the arrows. . I have no problem for experimentalists to draw the arrows based on their empirical knowledge. They do until they cannot. Further, by the empirical intuition, they often know when they should draw the arrows backward toward less positive (or more negative) potential such as in reverse reactions, which are also normal reactions upon a switch. . A theory is totally different. That "electron flow is always toward the positive potential" based on the state property without a specified limit at the theoretical level is strictly false. If it were true, there would not be any polar molecules in this nature! A referee of my JPC comment said this: "It is true that in the absence of other (orbital-dependent) factors...." Then this and the other referee wrote a lot to explain how orbitals are useful and complementary.... And one said "Frontier molecular orbital theory works ...except when it doesn't".... . The history and the reality tell me a valid theoretical task is to provide solid data to prove the physical event - electrons shift towards positive potential that does take place in a particular reaction. It is valueless to just reiterate the empirical hypothesis that is denied by the orbital control theories deeply rooted in the mighty chemical community. . Neither DFT nor AIM has provided a solution for the unusual dynamic complexity of cycloadditions, although I personally think that both DFT and AIM deserve the best award in the world. The reality is that we often cannot find tools to calculate what we need. Therefore, computational and theoretical chemists are needed as soon as we can recognize the challenges and controversies. If some one claims an "attractive" approach without a limit, another one must ask whether more works are needed and why. That would be a valuable and productive way to conduct theoretical science. . Thanks to every one for attention. . Sengen ____________________________________________________________________________________ Don't let your dream ride pass you by. Make it a reality with Yahoo! Autos. http://autos.yahoo.com/index.html