From owner-chemistry@ccl.net Sun Sep 26 00:03:00 2010 From: "Grigoriy Zhurko reg_zhurko,+,chemcraftprog.com" To: CCL Subject: CCL: CIF format Message-Id: <-42834-100925144027-30027-PvGgqO7L8yCUPoaohBCZ6g/a\server.ccl.net> X-Original-From: Grigoriy Zhurko Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Sat, 25 Sep 2010 22:40:18 -0700 MIME-Version: 1.0 Sent to CCL by: Grigoriy Zhurko [reg_zhurko*|*chemcraftprog.com] > Sent to CCL by: Marcel Swart [marcel.swart-x-icrea.cat] > See: > http://www.ccdc.cam.ac.uk/products/mercury/ I know about this program but I need not a program but algorithm for computing the coordinates of all atoms. I want to implement CIF visualization in Chemcraft. Besides that, Mercury 2.3 was unable to open my CIF files from the zeolite database ("Could not read symmetry operator" is shown). Grigoriy Zhurko. > On Sep 25, 2010, at 10:17 PM, Grigoriy Zhurko > reg_zhurko**chemcraftprog.com wrote: >> Dear All, >> I need to visualize structures from crystallographic information files (.cif). I know how to recalculate >> fractional coordinates into Cartesian. As far as I understand, in the section "_atom_site_fract_x" (y,z) only the >> coordinates of symmetry unique atoms are printed. How can they be duplicated to obtain the full structure? I tried to >> recalculate the fractional coordinates according to the "_symmetry_equiv_pos_as_xyz" section, and duplicate atoms >> corresponding to the number of lines in this section. E.g. in the attached sample file there are 4 atoms in the >> "_atom_site_fract" section and 8 lines in the "_symmetry_equiv_pos_as_xyz" section, so I got 4*8=32 atoms. But the >> actual number of atoms to be visualized is much bigger (according to the Java applet in the database of zeolite >> structures (http://www.iza-structure.org/databases/) from where this CIF file was taken). And the coordinates do not >> look correct. How can the CIF file be correctly visualized? >> I attach the source CIF file, the XYZ file with 4 atoms from the cif file, the XYZ file with 32 duplicated atoms, >> and the file taken from the Jave applet with correct structure (251 atoms). >> >> Grigoriy Zhurko. >> www.chemcraftprog.com From owner-chemistry@ccl.net Sun Sep 26 09:56:01 2010 From: "david.anick[a]rcn.com" To: CCL Subject: CCL:G: freezen dihedrals in five-membered rings Message-Id: <-42835-100925234148-27940-cy9PbAnPL6H0G4Vcf8VcmA_+_server.ccl.net> X-Original-From: Content-Type: multipart/alternative; boundary="-----073d0477c8d0948e272e0d7b7badad3e" Date: Sat, 25 Sep 2010 23:41:36 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: [david.anick_+_rcn.com] -------073d0477c8d0948e272e0d7b7badad3e Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable -------073d0477c8d0948e272e0d7b7badad3e Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hello Reynier,

If you have experimental values for th= e five dihedral angles, then these values come with error bars.  Yo= u cannot expect the five numbers to be compatible exactly as given. = ; Going back to the planar example, if your experimental error is +/- 1 = degree, which would be very good accuracy for such a measurement, your e= xperimental set could be {0,0,0,0,1}, which as we have seen, would be "i= mpossible" when combined.

It sounds to me like what you would wan= t to to is the following.  Fixing the known lengths of each bond in= your ring and the 3-atom angles,  do not seek a geometry that matc= hes all 5 dihedrals perfectly, but instead seek the geometry that minimi= zes the sum of the squares of the differences between its dihedrals and = the target dihedrals.  This is a strictly mathematical problem that= would not use Gaussian at all.  Once you have the "optimum" geomet= ry, i.e. the geometry that most closely matches your five numbers accord= ing to a least-squares criterion, you can then do a single-point calc us= ing Gaussian to see what its energy is.  Or, use the dihedrals that= describe the least-squares geometry and do a constrained opt from there= , but I don't think the geometry will change very much.

Peace,David
---- Original message ----

= Date: Sat, 25 Sep 2010 15:11:33 +0200
From: "Reynier Su= ardiaz del R=EDo reynier.suardiaz^^gmail.com" <owner-chemistry-,-ccl.ne= t>
Subject: CCL:G: freezen dihedrals in five-membered rings=
To: "Anick, David " <david.anick-,-rcn.com>
Dear David

Thanks for your answer. You are right at all, the di= hedrals are coupled and the value of one of them depends of the value os= the others, so you can not aspire to have any five values of dihedral. = Certainly, if you have a planar ring you can not change one dihedral (fr= om its 0 degree value) and keeping the rest in that planar form because = they have to change to be a possible geometry. What I am doing is giving= to the dihedral experimental values, so this combinations of dihedral a= re possible. I am not changing one dihedral value and keeping the rest i= n their previous values (sorry if I was not clear enough). But, even cha= nging the five dihedrals to a very similar possible values, the calculat= ion is ending with that error.
I think gaussian is not recognizing th= is new combinations of dihedrals as possible geometries. If I keep froze= n only two dihedral the calculation ends ok but the final obtained confo= rmation have not the five dihedral values that I want (only the two froz= en, the other three change a little). What I want to do is to obtain geo= metrically optimized conformations with the experimental values of the f= ive dihedrals and them, calculate properties. In this way I can see how = this property depends on the puckering of the ring.
I keep working on= it, many thanks for your comments, they are very usefull to me.

= All the best

Reynier

On Sat, Sep 25, 2010 at 5:01 AM, <= david.anick{}rcn.com> wrote:
Dear Reynier,

What is hap= pening is that when you have a ring, you can't just make the
dihedral= angles anything you want, because there are mathematical relations amon= g them.  To see this, consider a special case where all the atoms l= ie in a plane.  All five dihedral angles equal 0.  If you cons= train all five angles to be zero, Gaussian is happy to optimize this.&nb= sp; Now suppose you change one of the angles, even if you only change it= to +1 degree.  It becomes geometrically IMPOSSIBLE.  Because = four of the five dihedrals are still zero, all five atoms are still forc= ed to lie in a single plane.  Then a mathematical consequence is th= at the fifth dihedral is automatically zero also.  If you tell it t= o make that dihedral equal to +1, you are asking Gaussian to find a geom= etry that mathematically cannot exist.  Guess what: Gaussian cannot= do it, and gives you an error message.  The error message is appro= priate: "error imposing constraints".


If you want to change o= ne dihedral angle a little, you must allow some of the other four dihedr= al angles to adapt to the change.  If you work a little with this, = you will see that two dihedral angles essentially fix a five-member ring= . (This is technically true only if the bond lengths and bond angles are= also fixed, but it is hard to adapt bond lengths and angles to accommod= ate changing dihedral angles.)  Try this: change the dihedral angle= you want to change, and remove three of the other constraints, so that = you are specifying only two of the five dihedral angles.  I think G= aussian will be happy with that and will be able to converge.  If t= hat works maybe you can try specifying three of the dihedrals, or concei= vably, four, if the changes are very small.


You need to think= about what is the question you are trying to answer.  If it's abou= t the flexibility of the ring, your best approach may be to constrain ju= st one dihedral, and let the rest of the ring adapt as it needs to.
<= br>
I hope this has been helpful.
Peace,
David Anick PhD MD
=
---- Original message ----

Date: Fri, 24 Sep 2010 21:27:14 +0200<= br>From: "Reynier Suardiaz del R=EDo reynier.suardiaz!^!gmail.com" <owner-chemistry{}ccl.n= et>

Subject: CCL:G: freezen dihedrals in five-membe= red rings
<= b>To: "Anick, David " <david.anick{}rcn.com>

Dear D. = Close


Many thanks for your answer, you was right. I typed the= values of the dihedrals with 6 decimal places exactly matching with tho= se of the input structure. Doing this, the geometry optimization have fi= nished without problem in a few iterations. Now what I would like to do = is the following: I want to generate diferent conformations of this fura= nose ring by changing the dihedrals (between permitted values without br= eaking of the ring) and partially optimize this structures (obtained by = slightly changing the dihedral values) and keeping frozen the five dihed= rals. When I try to do this using redundant coordinates in gaussian I ob= tained the same error message than before:


-------------
&= nbsp;Iteration 99 RMS(Cart)=3D  0.00005822 RMS(Int)=3D  0.0095= 5580
 Iteration100 RMS(Cart)=3D  0.00005748 RMS(Int)=3D&nbs= p; 0.00959825
 New curvilinear step not converged.
 Erro= r imposing constraints
 Error termination via Lnk1e in C:\G03W\l= 101.exe at Fri Sep 24 21:05:06 2010.
 Job cpu time:  0 days=   0 hours  0 minutes  1.0 seconds.
 File lengths = (MBytes):  RWF=3D      7 Int=3D  = ;    0 D2E=3D      0 Chk=3D = ;     8 Scr=3D      1
--= ------------

even if I only change one dihedral from its original= value (at the input geometry) in less than one degree,  the calcul= ation ends with the above error message.
Does anybody knows how to do= this in gaussian, I mean, changing the dihedral angles of a five memebe= red ring (from its text input file) and to performe a partial geometrica= l optimization with diferent dihedral angles, other than the one of the = input geometry?

any comment or suggestions are welcome.

th= anks in advance and with very best regards

Reynier


2010/9/22 Close, David M. CLOSED~!~mail.etsu.edu <owner-chemistry]*[ccl.net>


Sent t= o CCL by: "Close, David M." [CLOSED#,#mail.etsu.edu]
Reynier:
 There is no li= mit to how many dihedrals you can freeze.  The problem is that you = typed something wrong.  Notice that the program tried 99 iterations= to fit you frozen coordiate information into the optimization routine.<= br>


Either you connected the coordinates incorrectly, or did = not have enough precision in the frozen coordinate.
So if the input l= ine has something like 10 5 6 8   31.3, first look at the string 10= 5 6 8 and make sure this is correct.  The use a graphics program t= o examine the actual dihedral geometry.  Run through the 4 atoms in= the string 10 5 6 8 and see what the graphic program thinks the dihedra= l angle actually is.  Copy the value to 5-6 decimal places and re e= nter the data.



 If this doesn't work, then you have= to use trial and error.  You said that freezing 2 dihedrals works.=  But how many iterations did it take?  I would expect only 2-= 3.  If more, then refine the coordinates, and then add a third froz= en dihedral.  You can quickly find the offending entry when the opt= imization routine bombs.



 Regards, Dave Close.
<= br>________________________________________
> From: owner-chemistr= y+closed=3D=3Detsu.edu= [A]ccl.net [owner-chemi= stry+closed=3D=3Detsu.edu<= /a>[A]ccl.net] on behal= f of Reynier Suard az reynier.suardiaz(a)gmail.com [owner-chemistry[A]ccl.net]



Sent: Wednesday, Septe= mber 22, 2010 10:49 AM
To: Close, David M.
Subject: CCL:G: freezen= dihedrals in five-membered rings

Sent to CCL by: "Reynier &= nbsp;Suard  az" [reynier.suardiaz]_[gmail.com]
Dear All

I want to generate a l= ot of conformations of furanose ring (or cyclopentane?) and later partia= lly optimize them but keeping frozen the dihedral angles. I am trying to= use redundant coordinates in gaussian writing at the end of the input g= aussian file the desired dihedrals to keep frozen. I am receiving an err= or message when i try to keep frozen more than two dihedral angles (of t= he ring) at the same time. For example if I try to froze the five dihedr= als of the ring I get the following message:




------ Iteration 99 RMS(Cart)=3D  0.00001156 RMS(Int)=3D  0.0= 0309967
 Iteration100 RMS(Cart)=3D  0.00001134 RMS(Int)=3D =  0.00310385
 New curvilinear step not converged.
 E= rror imposing constraints
 Error termination via Lnk1e in C:\G03= W\l101.exe at Mon Sep 20 17:48:17 2010.
 Job cpu time:  0 d= ays  0 hours  0 minutes  1.0 seconds.
 File lengt= hs (MBytes):  RWF=3D      7 Int=3D     &nb= sp;0 D2E=3D      0 Chk=3D      7 Scr=3D &n= bsp;    1
---------

I receive this error message eve= n when I try to freeze the dihedral at the same value they already have = in the initial structure.

Is not possible what am I trying to do?= How can I overcome this problem with gaussian? Is there any other possi= bility to do this kind of partial optimization in five-membered rings? N= ote that I can not freeze all the dihedrals using optimization in intern= al coordinates (opt=3Dz-matrix with a separate input section of "constan= ts") because of to define a z-matrix of a five-membered ring are necesar= y only two dihedrals, so I have to use redundants.



any co= mments or sugestions would be appreciatte

thanks in advance and v= ery best regards

Reynierhttp://www.ccl.net/cgi-bin= /ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://= www.ccl.net/spammers.txt



=


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-------073d0477c8d0948e272e0d7b7badad3e-- From owner-chemistry@ccl.net Sun Sep 26 10:31:01 2010 From: "VITORGE Pierre 094605 Pierre.VITORGE*_*cea.fr" To: CCL Subject: CCL:G: freezen dihedrals in five-membered rings Message-Id: <-42836-100926045951-25322-eVSsykVV6fwoYB7zBlM3Ug-$-server.ccl.net> X-Original-From: "VITORGE Pierre 094605" Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01CB5D59.14A2E62A" Date: Sun, 26 Sep 2010 10:59:06 +0200 MIME-Version: 1.0 Sent to CCL by: "VITORGE Pierre 094605" [Pierre.VITORGE..cea.fr] This is a multi-part message in MIME format. ------_=_NextPart_001_01CB5D59.14A2E62A Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Reynier, =20 you initially wrote "Note that I can not freeze all the dihedrals using optimization in = internal coordinates (opt=3Dz-matrix with a separate input section of = "constants") because of to define a z-matrix of a five-membered ring are = necesary only two dihedrals, so I have to use redundants." which more or less means the same thing as written by David : "What is happening is that when you have a ring, you can't just make the = dihedral angles anything you want, because there are mathematical = relations among them." In your case I would indeed use "opt=3Dz-matrix" to generate a relaxed = (partial) potential energy surface (PES), for this you can use the = option s (scan) for giving the values of the dihedral angle you want to = scan. The result should depend on the way you build the z-matrix. If it = works, you will see how changing your scanned dihedral angle, modify = other angles and distances. You can quickly test as I did below, using = Molden to build the z-matrix and then scanning one dihedral angle: you = can build the z-matrix in other ways, start to scan another dihedral = angle, of course use a more correct level of calculation, then = eventually scan 2 angles... The example below took less than 3 minutes, I changed dih4 from -17.3 = to 2.7, then 22.7 etc (dih4 -17.3071 S 9 20.), the ring broke at = 82.7 =20 %chk=3Dfuranose.chk #p am1 opt(z-matrix,maxcycle=3D111) =20 furanose =20 0 1 o c 1 co2 c 2 cc3 1 cco3 c 3 cc4 2 ccc4 1 dih4 c 4 cc5 3 ccc5 2 dih5 o 2 oc6 3 occ6 4 dih6 h 6 ho7 2 hoc7 3 dih7 o 3 oc8 2 occ8 1 dih8 h 8 ho9 3 hoc9 2 dih9 o 4 oc10 3 occ10 2 dih10 h 10 ho11 4 hoc11 3 dih11 c 5 cc12 4 ccc12 3 dih12 o 12 oc13 5 occ13 4 dih13 h 13 ho14 12 hoc14 5 dih14 c 12 cc15 5 ccc15 4 dih15 h 15 hc16 12 hcc16 5 dih16 h 15 hc17 12 hcc17 5 dih17 o 15 oc18 12 occ18 5 dih18 h 18 ho19 15 hoc19 12 dih19 h 2 hc20 3 hcc20 4 dih20 h 3 hc21 2 hcc21 1 dih21 h 4 hc22 3 hcc22 2 dih22 h 5 hc23 4 hcc23 3 dih23 h 12 hc24 5 hcc24 4 dih24 =20 co2 1.4277 cc3 1.5431 cco3 107.4811 cc4 1.5508 ccc4 104.7189 dih4 -17.3071 S 9 20. cc5 1.5443 ccc5 105.2894 dih5 7.8112 oc6 1.4004 occ6 110.4122 dih6 96.8047 ho7 0.9668 hoc7 107.0058 dih7 188.7133 oc8 1.4085 occ8 109.3195 dih8 -138.1141 ho9 0.967 hoc9 106.1938 dih9 177.812 oc10 1.4056 occ10 111.8011 dih10 132.7332 ho11 0.9691 hoc11 108.3076 dih11 294.4696 cc12 1.5344 ccc12 114.086 dih12 123.7438 oc13 1.4145 occ13 110.6185 dih13 293.5559 ho14 0.9686 hoc14 106.8956 dih14 285.6612 cc15 1.532 ccc15 111.3662 dih15 169.946 hc16 1.1235 hcc16 109.758 dih16 189.6751 hc17 1.1209 hcc17 110.2038 dih17 310.9579 oc18 1.4121 occ18 111.3377 dih18 74.5393 ho19 0.9668 hoc19 107.5904 dih19 296.006 hc20 1.1219 hcc20 113.687 dih20 224.6181 hc21 1.1246 hcc21 109.5548 dih21 100.9015 hc22 1.1256 hcc22 110.3756 dih22 248.6248 hc23 1.1238 hcc23 109.8069 dih23 247.6616 hc24 1.127 hcc24 108.6862 dih24 48.1857 =20 =20 =20 =20 -- Pierre Vitorge Directeur de recherche CEA Laboratoire Analyse et Modelisation pour la Biologie et l Environnement, = LAMBE, UMR 8587, CEA, Univ Evry, CNRS, Bd. Francois Mitterrand, Bat. Maupertuis, s 02=20 F-91025 Evry, France tel.01.69.47.01.40 (+33.1.69.47.01.40) pierre.vitorge(-)univ-evry.fr http://www.lambe.univ-evry.fr/pvitorge = =20 http://www.vitorge.name =20 -- CEA, DEN, Saclay, DPC, SECR, LSRM=20 Bat.391 Pe.121 F-91191 Gif-sur-Yvette, France. tel.01.69.08.32.65 (+33.1.69.08.32.65) ________________________________ De : owner-chemistry+pierre.vitorge=3D=3Dcea.fr(-)ccl.net = [mailto:owner-chemistry+pierre.vitorge=3D=3Dcea.fr(-)ccl.net] De la part = de David Pensak pensak^^^udel.edu Envoy=E9 : samedi 25 septembre 2010 22:39 =C0 : VITORGE Pierre 094605 Objet : CCL:G: freezen dihedrals in five-membered rings =20 I hate to be showing my age, but long long time ago QCPE had a program = called PUCKER which I think did everything you want in terms of = coordinate generation. I don't think QCPE is still in operation but = someone must have a copy of the code sitting on a disk somewhere. The = mathematics was worked out by Cremer and Pople at least 25 years ago. =20 David Pensak =20 On Sep 25, 2010, at 9:09 AM, Reynier Suardiaz del R=EDo = reynier.suardiaz]|[gmail.com wrote: Dear David Thanks for your answer. You are right at all, the dihedrals are coupled = and the value of one of them depends of the value os the others, so you = can not aspire to have any five values of dihedral. Certainly, if you = have a planar ring you can not change one dihedral (from its 0 degree = value) and keeping the rest in that planar form because they have to = change to be a possible geometry. What I am doing is giving to the = dihedral experimental values, so this combinations of dihedral are = possible. I am not changing one dihedral value and keeping the rest in = their previous values (sorry if I was not clear enough). But, even = changing the five dihedrals to a very similar possible values, the = calculation is ending with that error. I think gaussian is not recognizing this new combinations of dihedrals = as possible geometries. If I keep frozen only two dihedral the = calculation ends ok but the final obtained conformation have not the = five dihedral values that I want (only the two frozen, the other three = change a little). What I want to do is to obtain geometrically optimized = conformations with the experimental values of the five dihedrals and = them, calculate properties. In this way I can see how this property = depends on the puckering of the ring. I keep working on it, many thanks for your comments, they are very = usefull to me. All the best Reynier On Sat, Sep 25, 2010 at 5:01 AM, > wrote: Dear Reynier, What is happening is that when you have a ring, you can't just make the dihedral angles anything you want, because there are mathematical = relations among them. To see this, consider a special case where all = the atoms lie in a plane. All five dihedral angles equal 0. If you = constrain all five angles to be zero, Gaussian is happy to optimize = this. Now suppose you change one of the angles, even if you only change = it to +1 degree. It becomes geometrically IMPOSSIBLE. Because four of = the five dihedrals are still zero, all five atoms are still forced to = lie in a single plane. Then a mathematical consequence is that the = fifth dihedral is automatically zero also. If you tell it to make that = dihedral equal to +1, you are asking Gaussian to find a geometry that = mathematically cannot exist. Guess what: Gaussian cannot do it, and = gives you an error message. The error message is appropriate: "error = imposing constraints". If you want to change one dihedral angle a little, you must allow some = of the other four dihedral angles to adapt to the change. If you work a = little with this, you will see that two dihedral angles essentially fix = a five-member ring. (This is technically true only if the bond lengths = and bond angles are also fixed, but it is hard to adapt bond lengths and = angles to accommodate changing dihedral angles.) Try this: change the = dihedral angle you want to change, and remove three of the other = constraints, so that you are specifying only two of the five dihedral = angles. I think Gaussian will be happy with that and will be able to = converge. If that works maybe you can try specifying three of the = dihedrals, or conceivably, four, if the changes are very small. You need to think about what is the question you are trying to answer. = If it's about the flexibility of the ring, your best approach may be to = constrain just one dihedral, and let the rest of the ring adapt as it = needs to. I hope this has been helpful. Peace, David Anick PhD MD ---- Original message ---- Date: Fri, 24 Sep 2010 21:27:14 +0200 > From: "Reynier Suardiaz del R=EDo reynier.suardiaz!^!gmail.com = " > Subject: CCL:G: freezen dihedrals in five-membered rings To: "Anick, David " > Dear D. Close Many thanks for your answer, you was right. I typed the values of the = dihedrals with 6 decimal places exactly matching with those of the input = structure. Doing this, the geometry optimization have finished without = problem in a few iterations. Now what I would like to do is the = following: I want to generate diferent conformations of this furanose = ring by changing the dihedrals (between permitted values without = breaking of the ring) and partially optimize this structures (obtained = by slightly changing the dihedral values) and keeping frozen the five = dihedrals. When I try to do this using redundant coordinates in gaussian = I obtained the same error message than before: ------------- Iteration 99 RMS(Cart)=3D 0.00005822 RMS(Int)=3D 0.00955580 Iteration100 RMS(Cart)=3D 0.00005748 RMS(Int)=3D 0.00959825 New curvilinear step not converged. Error imposing constraints Error termination via Lnk1e in C:\G03W\l101.exe at Fri Sep 24 21:05:06 = 2010. Job cpu time: 0 days 0 hours 0 minutes 1.0 seconds. File lengths (MBytes): RWF=3D 7 Int=3D 0 D2E=3D 0 = Chk=3D 8 Scr=3D 1 -------------- even if I only change one dihedral from its original value (at the input = geometry) in less than one degree, the calculation ends with the above = error message. Does anybody knows how to do this in gaussian, I mean, changing the = dihedral angles of a five memebered ring (from its text input file) and = to performe a partial geometrical optimization with diferent dihedral = angles, other than the one of the input geometry? any comment or suggestions are welcome. thanks in advance and with very best regards Reynier 2010/9/22 Close, David M. CLOSED~!~mail.etsu.edu = > =09 =09 Sent to CCL by: "Close, David M." [CLOSED#,#mail.etsu.edu = ] Reynier: There is no limit to how many dihedrals you can freeze. The problem = is that you typed something wrong. Notice that the program tried 99 = iterations to fit you frozen coordiate information into the optimization = routine. =09 =09 Either you connected the coordinates incorrectly, or did not have = enough precision in the frozen coordinate. So if the input line has something like 10 5 6 8 31.3, first look at = the string 10 5 6 8 and make sure this is correct. The use a graphics = program to examine the actual dihedral geometry. Run through the 4 = atoms in the string 10 5 6 8 and see what the graphic program thinks the = dihedral angle actually is. Copy the value to 5-6 decimal places and re = enter the data. =09 =09 If this doesn't work, then you have to use trial and error. You said = that freezing 2 dihedrals works. But how many iterations did it take? = I would expect only 2-3. If more, then refine the coordinates, and then = add a third frozen dihedral. You can quickly find the offending entry = when the optimization routine bombs. =09 =09 Regards, Dave Close. =09 ________________________________________ > From: owner-chemistry+closed=3D=3Detsu.edu = [A]ccl.net [owner-chemistry+closed=3D=3Detsu.edu = [A]ccl.net ] on behalf of Reynier = Suard az reynier.suardiaz(a)gmail.com = [owner-chemistry[A]ccl.net ] =09 =09 Sent: Wednesday, September 22, 2010 10:49 AM To: Close, David M. Subject: CCL:G: freezen dihedrals in five-membered rings =09 Sent to CCL by: "Reynier Suard az" [reynier.suardiaz]_[gmail.com = ] Dear All =09 I want to generate a lot of conformations of furanose ring (or = cyclopentane?) and later partially optimize them but keeping frozen the = dihedral angles. I am trying to use redundant coordinates in gaussian = writing at the end of the input gaussian file the desired dihedrals to = keep frozen. I am receiving an error message when i try to keep frozen = more than two dihedral angles (of the ring) at the same time. For = example if I try to froze the five dihedrals of the ring I get the = following message: =09 =09 =09 ------ Iteration 99 RMS(Cart)=3D 0.00001156 RMS(Int)=3D 0.00309967 Iteration100 RMS(Cart)=3D 0.00001134 RMS(Int)=3D 0.00310385 New curvilinear step not converged. Error imposing constraints Error termination via Lnk1e in C:\G03W\l101.exe at Mon Sep 20 17:48:17 = 2010. Job cpu time: 0 days 0 hours 0 minutes 1.0 seconds. File lengths (MBytes): RWF=3D 7 Int=3D 0 D2E=3D 0 = Chk=3D 7 Scr=3D 1 --------- =09 I receive this error message even when I try to freeze the dihedral at = the same value they already have in the initial structure. =09 Is not possible what am I trying to do? How can I overcome this problem = with gaussian? Is there any other possibility to do this kind of partial = optimization in five-membered rings? Note that I can not freeze all the = dihedrals using optimization in internal coordinates (opt=3Dz-matrix = with a separate input section of "constants") because of to define a = z-matrix of a five-membered ring are necesary only two dihedrals, so I = have to use redundants. =09 =09 any comments or sugestions would be appreciatte =09 thanks in advance and very best regards = Reynierhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/= chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt = =20 =09 =09 =09 =09 -=3D This is automatically added to each message by the mailing script = =3D- =09 =09 =09 E-mail to subscribers: CHEMISTRY]*[ccl.net = or use:=09 E-mail to administrators: CHEMISTRY-REQUEST]*[ccl.net = or use=09http://www.ccl.net/chemistry/sub_unsub.shtml =09= =20 =09=09=09 =09=09=09 =09 --=20 reynier http://rincon.uam.es/dir?cw=3D331069946289062 --=20 reynier http://rincon.uam.es/dir?cw=3D331069946289062 =20 ------_=_NextPart_001_01CB5D59.14A2E62A Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Reynier,

 =

you initially = wrote

"Note that I can not freeze all the dihedrals using optimization in internal coordinates (opt=3Dz-matrix with a separate input section of "constants") because of to define a z-matrix of a = five-membered ring are necesary only two dihedrals, so I have to use redundants."

which more or = less means the same thing as written by David :

"What is happening is that when you have a ring, you can't just make the = dihedral angles anything you want, because there are mathematical relations among = them."

In your case I = would indeed use "opt=3Dz-matrix" to generate a = relaxed (partial) potential energy surface (PES), for this you can use the option s (scan) = for giving the values of the dihedral angle you want to scan. The result = should depend on the way you build the z-matrix. If it works, you will see how changing your scanned dihedral angle, modify other angles and distances. = You can quickly test as I did below, using Molden to build the z-matrix and = then scanning one dihedral angle: you can build the z-matrix in other ways, start to = scan another dihedral angle, of course use a more correct level of = calculation, then eventually scan 2 angles...

The example = below took less than 3 minutes, I changed =A0dih4 =A0from -17.3 to 2.7, then 22.7 = etc (dih4=A0=A0=A0 -17.3071=A0=A0 = S=A0=A0 9 20.), the ring broke at 82.7

 =

%chk=3Dfuranose.chk

#p = am1

opt(z-matrix,maxcycle=3D111)

 

furanose

 

0 = 1

=A0o

=A0c=A0=A0 1 co2

=A0c=A0=A0 2 cc3=A0=A0=A0=A0=A0=A0=A0 1 cco3

=A0c=A0=A0 3 cc4=A0=A0=A0=A0=A0=A0=A0 2 ccc4=A0=A0=A0=A0=A0=A0=A0=A0 1 dih4

=A0c=A0=A0 4 cc5=A0=A0=A0=A0=A0=A0=A0 3 ccc5=A0=A0=A0=A0=A0=A0=A0=A0 2 dih5

=A0o=A0=A0 2 oc6=A0=A0=A0=A0=A0=A0=A0 3 occ6=A0=A0=A0=A0=A0=A0=A0=A0 4 dih6

=A0h=A0=A0 6 ho7=A0=A0=A0=A0=A0=A0=A0 2 hoc7=A0=A0=A0=A0=A0=A0=A0=A0 3 dih7

=A0o=A0=A0 3 oc8=A0=A0=A0=A0=A0=A0=A0 2 occ8=A0=A0=A0=A0=A0=A0=A0=A0 1 dih8

=A0h=A0=A0 8 ho9=A0=A0=A0=A0=A0=A0=A0 3 hoc9=A0=A0=A0=A0=A0=A0=A0=A0 2 dih9

=A0o=A0=A0 4 oc10=A0=A0=A0=A0=A0=A0 3 occ10=A0=A0=A0=A0=A0=A0=A0 2 dih10

=A0h=A0 = 10 ho11=A0=A0=A0=A0=A0=A0 4 hoc11=A0=A0=A0=A0=A0=A0=A0 3 dih11

=A0c=A0=A0 5 cc12=A0=A0=A0=A0=A0=A0 4 ccc12=A0=A0=A0=A0=A0=A0=A0 3 dih12

=A0o=A0 = 12 oc13=A0 =A0=A0=A0=A0=A05 occ13=A0=A0=A0=A0=A0=A0=A0 4 dih13

=A0h=A0 = 13 ho14=A0=A0=A0=A0=A0 12 hoc14=A0=A0=A0=A0=A0=A0=A0 5 dih14

=A0c=A0 = 12 cc15=A0=A0=A0=A0=A0=A0 5 ccc15=A0=A0=A0=A0=A0=A0=A0 4 dih15

=A0h=A0 = 15 hc16=A0=A0=A0=A0=A0 12 hcc16=A0=A0=A0=A0=A0=A0=A0 5 dih16

=A0h=A0 = 15 hc17=A0=A0=A0=A0=A0 12 hcc17=A0=A0=A0=A0=A0=A0=A0 5 dih17

=A0o=A0 = 15 oc18=A0=A0=A0=A0=A0 12 occ18=A0=A0=A0=A0=A0=A0=A0 5 dih18

=A0h=A0 = 18 ho19=A0=A0=A0=A0=A0 15 hoc19=A0=A0=A0=A0=A0=A0 12 dih19

=A0h=A0=A0 2 hc20=A0=A0=A0=A0=A0=A0 3 hcc20=A0=A0=A0=A0=A0=A0=A0 4 dih20

=A0h=A0=A0 3 hc21=A0=A0=A0=A0=A0=A0 2 hcc21=A0=A0=A0=A0=A0=A0=A0 1 dih21

=A0h=A0=A0 4 hc22=A0=A0=A0=A0=A0=A0 3 hcc22=A0=A0=A0=A0=A0=A0=A0 2 dih22

=A0h=A0=A0 5 hc23=A0=A0=A0=A0=A0=A0 4 hcc23=A0=A0=A0=A0=A0=A0=A0 3 dih23

=A0h=A0 = 12 hc24=A0=A0=A0=A0=A0=A0 5 hcc24=A0=A0=A0=A0=A0=A0=A0 4 dih24

 

co2=A0=A0=A0=A0 1.4277

cc3=A0=A0=A0=A0 1.5431

cco3=A0=A0=A0 107.4811

cc4=A0=A0=A0=A0 1.5508

ccc4=A0=A0=A0 104.7189

dih4=A0=A0=A0 -17.3071=A0=A0 S=A0=A0 9 20.

cc5=A0=A0=A0=A0 1.5443

ccc5=A0=A0=A0 105.2894

dih5=A0=A0=A0 7.8112

oc6=A0=A0=A0=A0 1.4004

occ6=A0=A0=A0 110.4122

dih6=A0=A0=A0 96.8047

ho7=A0=A0=A0=A0 0.9668

hoc7=A0=A0=A0 107.0058

dih7=A0=A0=A0 188.7133

oc8=A0=A0=A0=A0 1.4085

occ8=A0=A0=A0 109.3195

dih8=A0=A0=A0 -138.1141

ho9=A0=A0=A0=A0 0.967

hoc9=A0=A0=A0 106.1938

dih9=A0=A0=A0 177.812

oc10=A0=A0=A0 1.4056

occ10=A0=A0 111.8011

dih10=A0=A0 132.7332

ho11=A0=A0=A0 0.9691

hoc11=A0=A0 108.3076

dih11=A0=A0 294.4696

cc12=A0=A0=A0 1.5344

ccc12=A0=A0 114.086

dih12=A0=A0 123.7438

oc13=A0=A0=A0 1.4145

occ13=A0=A0 110.6185

dih13=A0=A0 293.5559

ho14=A0=A0=A0 0.9686

hoc14=A0=A0 106.8956

dih14=A0=A0 285.6612

cc15=A0=A0=A0 1.532

ccc15=A0=A0 111.3662

dih15=A0=A0 169.946

hc16=A0=A0=A0 1.1235

hcc16=A0=A0 109.758

dih16=A0=A0 189.6751

hc17=A0=A0=A0 1.1209

hcc17=A0=A0 110.2038

dih17=A0=A0 310.9579

oc18=A0=A0=A0 1.4121

occ18=A0=A0 111.3377

dih18=A0=A0 74.5393

ho19=A0=A0=A0 0.9668

hoc19=A0=A0 107.5904

dih19=A0=A0 296.006

hc20=A0=A0=A0 1.1219

hcc20=A0=A0 113.687

dih20=A0=A0 224.6181

hc21=A0=A0=A0 1.1246

hcc21=A0=A0 109.5548

dih21=A0=A0 100.9015

hc22=A0=A0=A0 1.1256

hcc22=A0=A0 110.3756

dih22=A0=A0 248.6248

hc23=A0=A0=A0 1.1238

hcc23=A0=A0 109.8069

dih23=A0=A0 247.6616

hc24=A0=A0=A0 1.127

hcc24=A0=A0 108.6862

dih24=A0=A0 48.1857

 =

 =

 =

 

--
Pierre Vitorge

Directeur de recherche = CEA


Laboratoire Analyse et = Modelisation pour la Biologie et l Environnement, LAMBE, UMR 8587, CEA, Univ Evry, = CNRS,
Bd. Francois Mitterrand, Bat. Maupertuis, s 02 
F-91025 Evry, France
tel.01.69.47.01.40 (+33.1.69.47.01.40)
pierre.vitorge(-)univ-evry.fr
http://www.lambe.univ-evry.fr/pvitorge
http://www.vitorge.name
--
CEA, DEN, Saclay, DPC, SECR, LSRM 
Bat.391 Pe.121
F-91191 Gif-sur-Yvette, France.

tel.01.69.08.32.65 = (+33.1.69.08.32.65)

De : owner-chemistry+pierre.vitorge=3D=3Dcea.fr(-)ccl.net [mailto:owner-chemistry+pierre.vitorge=3D=3Dcea.fr(-)ccl.net] De la part de David Pensak pensak^^^udel.edu
Envoy=E9 : samedi 25 = septembre 2010 22:39
=C0 : VITORGE Pierre = 094605
Objet : CCL:G: = freezen dihedrals in five-membered rings

 

I hate to be showing my age, but long long time ago QCPE had a = program called PUCKER which I think did everything you want in terms of = coordinate generation.   I don't think QCPE is still in operation but someone = must have a copy of the code sitting on a disk somewhere.   The = mathematics was worked out by Cremer and Pople at least 25 years = ago.

 

David Pensak

 

On Sep 25, 2010, at 9:09 AM, Reynier Suardiaz del R=EDo reynier.suardiaz]|[gmail.com wrote:



Dear David

Thanks for your answer. You are right at all, the dihedrals are coupled = and the value of one of them depends of the value os the others, so you can not = aspire to have any five values of dihedral. Certainly, if you have a planar = ring you can not change one dihedral (from its 0 degree value) and keeping the = rest in that planar form because they have to change to be a possible geometry. = What I am doing is giving to the dihedral experimental values, so this = combinations of dihedral are possible. I am not changing one dihedral value and keeping = the rest in their previous values (sorry if I was not clear enough). But, = even changing the five dihedrals to a very similar possible values, the = calculation is ending with that error.
I think gaussian is not recognizing this new combinations of dihedrals = as possible geometries. If I keep frozen only two dihedral the calculation = ends ok but the final obtained conformation have not the five dihedral values = that I want (only the two frozen, the other three change a little). What I want = to do is to obtain geometrically optimized conformations with the experimental = values of the five dihedrals and them, calculate properties. In this way I can = see how this property depends on the puckering of the ring.
I keep working on it, many thanks for your comments, they are very = usefull to me.

All the best

Reynier

On Sat, Sep 25, 2010 at 5:01 AM, <david.anick%a%rcn.com> = wrote:

Dear Reynier,

What is happening is that when you have a ring, you can't just make = the
dihedral angles anything you want, because there are mathematical = relations among them.  To see this, consider a special case where all the = atoms lie in a plane.  All five dihedral angles equal 0.  If you = constrain all five angles to be zero, Gaussian is happy to optimize this.  Now = suppose you change one of the angles, even if you only change it to +1 = degree.  It becomes geometrically IMPOSSIBLE.  Because four of the five = dihedrals are still zero, all five atoms are still forced to lie in a single = plane.  Then a mathematical consequence is that the fifth dihedral is = automatically zero also.  If you tell it to make that dihedral equal to +1, you = are asking Gaussian to find a geometry that mathematically cannot = exist.  Guess what: Gaussian cannot do it, and gives you an error message.  = The error message is appropriate: "error imposing = constraints".

If you want to change one dihedral angle a little, you must allow some = of the other four dihedral angles to adapt to the change.  If you work a = little with this, you will see that two dihedral angles essentially fix a = five-member ring. (This is technically true only if the bond lengths and bond angles = are also fixed, but it is hard to adapt bond lengths and angles to = accommodate changing dihedral angles.)  Try this: change the dihedral angle you = want to change, and remove three of the other constraints, so that you are specifying only two of the five dihedral angles.  I think Gaussian = will be happy with that and will be able to converge.  If that works maybe = you can try specifying three of the dihedrals, or conceivably, four, if the = changes are very small.

You need to think about what is the question you are trying to = answer.  If it's about the flexibility of the ring, your best approach may be to = constrain just one dihedral, and let the rest of the ring adapt as it needs = to.

I hope this has been helpful.
Peace,
David Anick PhD MD

---- Original message ----


Date: Fri, 24 Sep 2010 = 21:27:14 +0200
From: "Reynier = Suardiaz del R=EDo reynier.suardiaz!^!gmail.com" <owner-chemistry%a%ccl.net>
Subject: CCL:G: freezen = dihedrals in five-membered rings

To: "Anick, David " <david.anick%a%rcn.com>

Dear D. Close

Many thanks for your answer, you was right. I typed the values of the = dihedrals with 6 decimal places exactly matching with those of the input = structure. Doing this, the geometry optimization have finished without problem in a few iterations. Now what I would like to do is the following: I want to = generate diferent conformations of this furanose ring by changing the dihedrals = (between permitted values without breaking of the ring) and partially optimize = this structures (obtained by slightly changing the dihedral values) and = keeping frozen the five dihedrals. When I try to do this using redundant = coordinates in gaussian I obtained the same error message than before:

-------------
 Iteration 99 RMS(Cart)=3D  0.00005822 RMS(Int)=3D  = 0.00955580
 Iteration100 RMS(Cart)=3D  0.00005748 RMS(Int)=3D  = 0.00959825
 New curvilinear step not converged.
 Error imposing constraints
 Error termination via Lnk1e in C:\G03W\l101.exe at Fri Sep 24 = 21:05:06 2010.
 Job cpu time:  0 days  0 hours  0 minutes  1.0 seconds.
 File lengths (MBytes):  RWF=3D      = 7 Int=3D      0 = D2E=3D      0 Chk=3D      8 = Scr=3D      1
--------------

even if I only change one dihedral from its original value (at the input geometry) in less than one degree,  the calculation ends with the = above error message.
Does anybody knows how to do this in gaussian, I mean, changing the = dihedral angles of a five memebered ring (from its text input file) and to = performe a partial geometrical optimization with diferent dihedral angles, other = than the one of the input geometry?
any comment or suggestions are welcome.

thanks in advance and with very best regards

Reynier

2010/9/22 Close, David M. CLOSED~!~mail.etsu.edu <owner-chemistry]*[ccl.net>



Sent to CCL by: "Close, David M." [CLOSED#,#mail.etsu.edu]
Reynier:
 There is no limit to how many dihedrals you can freeze.  The = problem is that you typed something wrong.  Notice that the program tried = 99 iterations to fit you frozen coordiate information into the optimization routine.


Either you connected the coordinates incorrectly, or did not have enough precision in the frozen coordinate.
So if the input line has something like 10 5 6 8   31.3, first look = at the string 10 5 6 8 and make sure this is correct.  The use a graphics = program to examine the actual dihedral geometry.  Run through the 4 atoms = in the string 10 5 6 8 and see what the graphic program thinks the dihedral = angle actually is.  Copy the value to 5-6 decimal places and re enter the = data.


 If this doesn't work, then you have to use trial and error. =  You said that freezing 2 dihedrals works.  But how many iterations did = it take?  I would expect only 2-3.  If more, then refine the coordinates, and then add a third frozen dihedral.  You can quickly = find the offending entry when the optimization routine bombs.


 Regards, Dave Close.

________________________________________
> From: owner-chemistry+closed=3D=3Detsu.edu[A]ccl.net = [owner-chemistry+closed=3D=3Detsu.edu[A]ccl.net] on behalf of Reynier Suard az = reynier.suardiaz(a)gmail.com = [owner-chemistry[A]ccl.net]


Sent: Wednesday, September 22, 2010 10:49 AM
To: Close, David M.
Subject: CCL:G: freezen dihedrals in five-membered = rings


Sent to CCL by: "Reynier  Suard  az" = [reynier.suardiaz]_[gmail.com]
Dear All

I want to generate a lot of conformations of furanose ring (or = cyclopentane?) and later partially optimize them but keeping frozen the dihedral = angles. I am trying to use redundant coordinates in gaussian writing at the end of = the input gaussian file the desired dihedrals to keep frozen. I am receiving an = error message when i try to keep frozen more than two dihedral angles (of the = ring) at the same time. For example if I try to froze the five dihedrals of = the ring I get the following message:



------
 Iteration 99 RMS(Cart)=3D  0.00001156 RMS(Int)=3D =  0.00309967
 Iteration100 RMS(Cart)=3D  0.00001134 RMS(Int)=3D =  0.00310385
 New curvilinear step not converged.
 Error imposing constraints
 Error termination via Lnk1e in C:\G03W\l101.exe at Mon Sep 20 = 17:48:17 2010.
 Job cpu time:  0 days  0 hours  0 minutes  1.0 seconds.
 File lengths (MBytes):  RWF=3D      7 Int=3D =      0 D2E=3D      0 Chk=3D      7 = Scr=3D      1
---------

I receive this error message even when I try to freeze the dihedral at = the same value they already have in the initial structure.

Is not possible what am I trying to do? How can I overcome this problem = with gaussian? Is there any other possibility to do this kind of partial optimization in five-membered rings? Note that I can not freeze all the dihedrals using optimization in internal coordinates (opt=3Dz-matrix = with a separate input section of "constants") because of to define a z-matrix of a five-membered ring are necesary only two dihedrals, so I = have to use redundants.


any comments or sugestions would be appreciatte

thanks in advance and very best regards

Reynierhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.= net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt



-=3D This is automatically added to each message by the mailing script = =3D-





--
reynier
http://rincon.uam.= es/dir?cw=3D331069946289062

 

------_=_NextPart_001_01CB5D59.14A2E62A-- From owner-chemistry@ccl.net Sun Sep 26 11:05:01 2010 From: "vandestreek#avmatsim.de" To: CCL Subject: CCL: CIF format Message-Id: <-42837-100926101402-317-fwbd616JxCCIVBSj8pwLhQ]|[server.ccl.net> X-Original-From: vandestreek*|*avmatsim.de Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Sun, 26 Sep 2010 16:13:47 +0200 MIME-Version: 1.0 Sent to CCL by: vandestreek%x%avmatsim.de Quoting "Grigoriy Zhurko reg_zhurko,+,chemcraftprog.com" : >> http://www.ccdc.cam.ac.uk/products/mercury/ > > I know about this program but I need not a program but algorithm > for computing the coordinates of all atoms. I want to implement CIF > visualization in Chemcraft. As a former Mercury developer I think I can give you some hints. The simple answer is, that you have to generate additional atoms from the asymmetric unit via the symmetry operators, then you have to check which (if any) of the newly generated atoms form bonds to your molecule. There are several implementation details that you have to be careful with: 1. When determining bonds, you must take the 3D periodicity into account. If an atom has fractional coordinates (-0.344, 1.225, 0.8790), then symmetry-related copies of that atom must also be present at (-0.344, 0.225, 0.8790), (0.656, 1.225, 0.8790), (0.656, -1.775, 0.8790), (-0.344, 1.225, 6.8790) etc. In other words, you can always add or subtract an integer from any fractional x, y or z coordinate. This is especially important if one or more of the atoms of the asymmetric unit are outside the unit cell, because in that case symmetry operators like inversions or mirror planes (in their standard forms as they appear in cifs) will generate atoms with coordinates at the other side of the unit cell (i.e. very far apart), even if some of their periodic copies may be close enough together to form a bond. 2. Compounds such as polymers, catena compounds or zeolites form infinite networks rather than discrete molecules. Since infinite structures cannot be displayed, you must choose an arbitrary cutoff. There is no "right" or "wrong", so your target of 251 atoms for the zeolite structure is arbitrary. One full unit cell, or one full unit cell + the fits atom outside the unit cell along each chemical bond are reasonable values. 3. Cifs may contain more than one molecule, for example because the crystal structure incorporated a solvent molecule (or several solvent molecules) or because the compound crystallised as a co-crystal or as a salt. The compound may also have multiple molecules in the asymmetric unit. 4. Some atoms are on special positions: one or more of the symmetry elements produce the same atom at the same position (for example if the atom is sitting on a mirror plane). These must be detected and removed: imagine the energies a QM program would produce for two atoms on top of each other. The user cannot see the second atom because it is in the exact same place as the first, so leaving in these atoms would be a very annoying "feature" of your algorithm. Because atomic coordinates in cif files are not exact, rounding errors must be taken into account. E.g an atom with coordinates (0, 0.333, 0) is probably on a three-fold axis and its exact coordinates are probably (0, 1/3, 0). The difference between 3 * 1/3 = 1 and 3 * 0.333 = 0.999 is a rounding error that your algorithm must cater for, otherwise you will have atoms that are only, say, 0.01 A apart. You should probably *first* convert to Cartesian coordinates, because that makes it easier to judge what chemically reasonable tolerance values are: a fractional difference of 0.001 is entirely reasonable if the unit-cell parameter for that coordinate is 1000 A, because 0.001 * 1000 A = 1 A, which is a C-H bond length. 5. All information about the entire crystal structure is contained in one unit cell: if you first normalise all fractional x, y and z coordinates to lie within [0,1) and you then apply all symmetry operators to all atoms in the asymmetric unit and you then normalise all fractional x, y and z coordinates of all symmetry-generated atoms to [0,1) and you then remove all duplicates, then you are guaranteed to have found all relevant atoms. Now you have to find bonds and to remove all molecules that are symmetry-related to other molecules, and you have to expand the problem cases from point 2 to something "chemically reasonable". When normalising to [0,1), bear in mind rounding errors: you are probably better off keeping all atoms between [-d,1+d], where d is something small like 0.0001, and then removing duplicates where you allow for 3D periodicity and rounding errors again: so -0.000003258, 0.000001825, 0.9999988234 and 1.00000578 are all equal within rounding errors. Most, if not all, of this is probably described somewhere, you may try the CCL archives or a google search. > Besides that, Mercury 2.3 was unable to open my CIF files from the > zeolite database ("Could not read symmetry operator" is shown). The symmetry operators in the file that you attached look like this: ' +x +y +z ' according to the cif specification ( http://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Isymmetry_equiv_pos_as_xyz.html ), commas should be used as delimiters, so the the line should have looked like this: ' +x, +y, +z ' (Actually, it is more usual to write it like: +x,+y,+z The single quotes are only necessary if whitespace in the form of spaces or tabs is present in the string.) But even when I change that, I still get two more error messages. First, the cif that you attached contains element symbol "T". Although this can be used to specify tritium, tritium is not recognised by Mercury and even if it was, this is not what is meant in your crystal structure: the atoms are meant to be Silicon (element symbol "Si"). Second, the space-group name and the space-group symmetry operators in your file are not consistent: the space-group name is Imma, but the symmetry operators specify space group Pmmb, a non-standard setting of space group Pmma. So which of these two is correct? If you try both in Mercury, you will see that symmetry operators in space group Pmmb only generate enough additional atoms from the asymmetric unit to fill half the unit cell: the other half is left empty. With the symmetry operators from space group Imma, which has twice as many symmetry operators as Pmmb, the entire unit cell is filled. This makes Imma the correct space group. (I looked at the symmetry operators and the I-centring has been omitted.) So the cif file that you attached, the format of the symmetry operators is incorrect, half of the symmetry operators are missing and the cif contains a non-existing element. Best wishes, -- Dr Jacco van de Streek Senior Scientist Avant-garde Materials Simulation Freiburg im Breisgau, Germany From owner-chemistry@ccl.net Sun Sep 26 14:17:01 2010 From: "Shirin Seifert shirin.seifert**gmail.com" To: CCL Subject: CCL:G: MQD Message-Id: <-42838-100926141625-16019-ofJpuvyGrxbJnMT9VgMt2A%%server.ccl.net> X-Original-From: Shirin Seifert Content-Type: multipart/alternative; boundary=0016364c71ada41a4404912d9b77 Date: Sun, 26 Sep 2010 21:46:17 +0330 MIME-Version: 1.0 Sent to CCL by: Shirin Seifert [shirin.seifert . gmail.com] --0016364c71ada41a4404912d9b77 Content-Type: text/plain; charset=ISO-8859-1 Dear All, I would like to study Molecular Quantum-dots in Gaussian. Could anyone introduce some instructive articles, text books, etc., on this topic? Thank you in advance. Best regards, S.S. --0016364c71ada41a4404912d9b77 Content-Type: text/html; charset=ISO-8859-1 Dear All,

I would like to study Molecular Quantum-dots in Gaussian. Could anyone introduce some instructive articles, text books, etc., on this topic?
Thank you in advance.

Best regards,
S.S.
--0016364c71ada41a4404912d9b77-- From owner-chemistry@ccl.net Sun Sep 26 22:33:00 2010 From: "Decai Yu decaiyu23]![yahoo.com" To: CCL Subject: CCL: freezing angle Error in internal coordinate system Message-Id: <-42839-100926222304-29681-s6+p1fC1wbMPMvr+t8SAow-x-server.ccl.net> X-Original-From: Decai Yu Content-Type: multipart/alternative; boundary="0-1161427098-1285554179=:6459" Date: Sun, 26 Sep 2010 19:22:59 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Decai Yu [decaiyu23[-]yahoo.com] --0-1161427098-1285554179=:6459 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear All, =A0 I am trying to do a partial=A0 geometry optimization. In my structures, I have a number of atoms fixed and I also have one angle = fixed. When I changed the value of the fixed angle from 135 to 180, the smaller an= gle runs are finished without error. But for angle value larger than 175, it can only run one step (a full SCF r= elaxation).=20 =A0 The program=A0ends with the following error: =A0 =A0GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad =A0Berny optimization. =A0NTrRot=3D=A0=A0 421 NTRed=3D=A0=A0 574 NAtoms=3D=A0=A0=A0 51 NSkip=3D=A0= =A0 421 IsLin=3DF =A0Error in internal coordinate system. I would appreciate any help or advice. =A0 Best Regards, =A0 Decai =A0=0A=0A=0A --0-1161427098-1285554179=:6459 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear All,
 
I am trying to do a partial  geometry optimization.
In my structures, I have a number of atoms fixed and I also have one a= ngle fixed.
When I changed the value of the fixed angle from 135 to 180, the small= er angle runs are finished without error.
But for angle value larger than 175, it can only run one step (a full = SCF relaxation).
 
The program ends with the following error:
 
 GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad= GradGrad
 Berny optimization.
 NTrRot=3D   421 NT= Red=3D   574 NAtoms=3D    51 NSkip=3D   = 421 IsLin=3DF
 Error in internal coordinate system.

I would = appreciate any help or advice.
 
Best Regards,
 
Decai
 

=0A= =0A --0-1161427098-1285554179=:6459--