From owner-chemistry@ccl.net Tue Sep 28 01:20:00 2010 From: "SUBHADEEP SAHA saha.subhadeep|-|gmail.com" To: CCL Subject: CCL:G: problem with fixing a bond Message-Id: <-42846-100927235413-5149-pt7kvjzBHPM8Vocc6i1qPw]|[server.ccl.net> X-Original-From: SUBHADEEP SAHA Content-Type: multipart/alternative; boundary=00c09f99e4d2c0e431049149cba6 Date: Tue, 28 Sep 2010 09:24:03 +0530 MIME-Version: 1.0 Sent to CCL by: SUBHADEEP SAHA [saha.subhadeep ~~ gmail.com] --00c09f99e4d2c0e431049149cba6 Content-Type: text/plain; charset=ISO-8859-1 Dear all, Very sorry for inconvenience. I am using Gaussian 03.In my input files some M(metal)-O-CH3 is present.I have frozen metal and oxygen atoms but C and H atoms are free.I have frozen the C-H bonds.Now the problem is M-O-CH3 angle deviates a lot in the output because it seems to me the oxygen atom of another M-O-CH3 attracts the H of CH3 group but doesn't detach from CH3 because of the constrains applied. Hope this gives some more light on my input and output. Regards Subhadeep On Tue, Sep 28, 2010 at 1:24 AM, Jim Kress ccl_nospam=kressworks.com < owner-chemistry(~)ccl.net> wrote: > What software are you using and what do your input and output files look > like? > > > > Jim > > > > *From:* owner-chemistry+ccl_nospam==kressworks.com..ccl.net [mailto: > owner-chemistry+ccl_nospam ==kressworks.com > ..ccl.net] *On Behalf Of *SUBHADEEP SAHA saha.subhadeep*gmail.com > *Sent:* Monday, September 27, 2010 11:04 AM > *To:* Kress, Jim > *Subject:* CCL: problem with fixing a bond > > > > > Dear all, > > I am trying to optimize(b3lyp/6-31g) a structure freezing almost 20 atoms > and 30 bonds.Now the problem is crashing after a running number of steps > giving the following error > > > > Iteration100 RMS(Cart)= 0.00000470 RMS(Int)= 0.01035587 > New curvilinear step not converged. > Error imposing constraints > > > > I checked the final configuration and got that the some of the groups(which > are > from the frozen bonds only,suppose I have frozen the C-H bonds of CH3 > groups) moves away from initial configuration after feeling some favorable > interaction elsewhere. > > I have checked CCL archives" > http://server.ccl.net/cgi-bin/ccl/message-new?2003+05+23+007".But did not > get any satisfactory solution to optimizing the structure keeping the > constrains(Whatever I have provided) same. > > Can anyone please suggest a solution? > > Thanks in advance... > > > Regards, > Subhadeep Saha > C/O Dr.Rahul Banerjee > Materials and Physical Chemistry Division > National Chemical Laboratory > Dr. Homi Bhabha Road > Pune:411008 > Maharasthra > India > Ph:+91-20-2590-2387 > +91-20-2590-2535 > +91-20-2590-2598 > -- Regards, Subhadeep Saha C/O Dr.Rahul Banerjee Materials and Physical Chemistry Division National Chemical Laboratory Dr. Homi Bhabha Road Pune:411008 Maharasthra India Ph:+91-20-2590-2387 +91-20-2590-2535 +91-20-2590-2598 --00c09f99e4d2c0e431049149cba6 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear all,

Very sorry for inconvenience.

I am using Gaussian 0= 3.In my input files=A0 some M(metal)-O-CH3 is present.I have frozen metal a= nd oxygen atoms but C and H atoms are free.I have frozen the C-H bonds.Now = the problem is M-O-CH3 angle deviates a lot in the output because it seems = to me the oxygen atom of another M-O-CH3 attracts the H of CH3 group but do= esn't detach from CH3 because of the constrains applied.
=A0Hope this gives some more light on my input and output.



R= egards

Subhadeep


On Tue, Sep = 28, 2010 at 1:24 AM, Jim Kress ccl_nospam=3Dkressworks.com <owner-chemistry(~)ccl.net> wrote:

What software are you using and what do your input and output files look like?

=A0

Jim

=A0

From:= owner-chemistry+ccl_nospam=3D=3Dkresswork= s.com..ccl.net [mailto:o= wner-chemistry+ccl_nospam=3D=3Dkressw= orks.com..ccl.net] = On Behalf Of SUBHADEEP SAHA saha.subhadeep*gmail.co= m
Sent: Monday, September 27, 2010 11:04 AM
To: Kress, Jim
Subject: CCL: problem with fixing a bond

=A0


Dear all,

I am trying to optimize(b3lyp/6-31g) a structure freezing almost 20 atoms a= nd 30 bonds.Now the problem=A0 is crashing after a running number of steps=A0 giving the following error



Iteration100 RMS(Cart)=3D=A0 0.00000470 RMS(Int)=3D=A0 0.01035587
=A0New curvilinear step not converged.
=A0Error imposing constraints



I checked the final configuration and got that the some of the groups(which= are > from the frozen bonds only,suppose I have frozen the C-H bonds of CH3 = groups) moves away from initial configuration after feeling some favorable interact= ion elsewhere.

I have checked CCL archives"http://server.ccl.net/cgi-= bin/ccl/message-new?2003+05+23+007".But did not get any satisfactory solution to optimizing the structure keeping t= he constrains(Whatever I have provided) same.

Can anyone please suggest a solution?

Thanks in advance...


Regards,
Subhadeep Saha
C/O Dr.Rahul Banerjee
Materials and Physical Chemistry Division
National Chemical Laboratory
Dr. Homi Bhabha Road
Pune:411008
Maharasthra
India
Ph:+91-20-2590-2387
=A0 =A0=A0 +91-20-2590-2535
=A0 =A0=A0 +91-20-2590-2598




--
Regards,
Subhadeep S= aha
C/O Dr.Rahul Banerjee
Materials and Physical Chemistry DivisionNational Chemical Laboratory
Dr. Homi Bhabha Road
Pune:411008
Maharasthra
India
Ph:+91-20-2590-2387
=A0 =A0=A0 +91-20-2590-2535<= br>=A0 =A0=A0 +91-20-2590-2598
--00c09f99e4d2c0e431049149cba6-- From owner-chemistry@ccl.net Tue Sep 28 02:05:00 2010 From: "Hyungjun Kim hyungjun96*o*kaist.ac.kr" To: CCL Subject: CCL: G09 TDDFT results analysis Message-Id: <-42847-100928020338-15155-6WziWYjpjAt+wlQwOjnxgQ-.-server.ccl.net> X-Original-From: "Hyungjun Kim" Date: Tue, 28 Sep 2010 02:03:37 -0400 Sent to CCL by: "Hyungjun Kim" [hyungjun96!A!kaist.ac.kr] Dear CCL members, This is Hyungjun Kim. I did a TDDFT calculation using B3LYP functional for the molecule which is the candidate for an OLED compound. The results is a little bit strange to me. **************************** Excited State 1: Triplet-A 1.8142 eV 683.40 nm f=0.0000 =2.000 205 -> 206 0.68419 205 <- 206 0.10509 **************************** I have never seen such excitations like 205<-206. (205 is HOMO and 206 is LUMO.) How do I analyze this result? Any suggestions will helpful to me. Thank you. From owner-chemistry@ccl.net Tue Sep 28 07:43:00 2010 From: "dharitri nil das dharitri.chem~!~gmail.com" To: CCL Subject: CCL:G: link died Message-Id: <-42848-100928051345-23990-quXDoKIT0lD9i1OBw+XIBg**server.ccl.net> X-Original-From: "dharitri nil das" Date: Tue, 28 Sep 2010 05:13:44 -0400 Sent to CCL by: "dharitri nil das" [dharitri.chem^-^gmail.com] I am doing optimization+frequency on [trans-RuCl4(1-methyl-1,2,4-triazole)(dmso-S)]anion in solvent phase.The program died after 17 days running. the job terminated with the following error message : Ideas are like rabbits.You get a couple and learn how to handle them, & pretty soon you have a dozen - John Steinbeck Error termination request processed by link 9999 Error termination via Lnkle in C:\G03W\l9999.exe at sat sep 25 16:03:30 2010 Job CPU time:17 days 4 hours 8 minutes 14.0 seconds. File length (MBytes):RWF= 493 int=0D2E=0chk=10scr INPUT= #opt=(tight,gdiis)ub3lyp/genECP scrf=(pcm,solvent=water)nosym geom=connectivity pop=regular freq yours faithfully Dharitri Das Department of Chemistry,Assam University Silchar-788011 email=dharitri.chem__gmail.com From owner-chemistry@ccl.net Tue Sep 28 09:40:00 2010 From: "=?ISO-8859-1?Q?Reynier_Suardiaz_del_R=EDo?= reynier.suardiaz(a)gmail.com" To: CCL Subject: CCL:G: freezen dihedrals in five-membered rings Message-Id: <-42849-100928085441-14192-OFUNW9gYltZiQct4YWPq3A~!~server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Reynier_Suardiaz_del_R=EDo?= Content-Type: multipart/alternative; boundary=00c09f93d5db9e7aef04915158c5 Date: Tue, 28 Sep 2010 14:54:30 +0200 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Reynier_Suardiaz_del_R=EDo?= [reynier.suardiaz _ gmail.com] --00c09f93d5db9e7aef04915158c5 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Patrick Thanks a lot for your answer. The idea of using the main conformers sound very well but what I really would like to do is, besides those conformers, generate much more at intermediate positions. What is really happening is that I thought if I change the dihedrals in Gaussian using redundant coordinates, the software would change all dihedrals (without problems because the combinations of dihedrals should be permitted) and performe a partial optimization in this new conformation. After that, I would write some simple code to automatically change the dihedrals to many permitted values (to do that, I need the mathematical relation between dihedrals) and to obtain many partially optimized conformations that I could use to calculate properties. That plan does not work.... :-( 1st Gaussian can only perform the partial optimization if you freeze the dihedrals at the same value of the input geometry, if you change this values even to other geometrically permitted combinations of dihedrals the calculations ends abnormally. 2nd I do not have the mathematical relation between the dihedrals in order to change one of them and predict the permitted values o= f the others. So I could try to "play" with the geometries trying to find suitable combinations in some way as suggested by Pierre or David (many thanks to both) or I can look for a code to generate many conformers of a five membered ring as PUCKER mentioned by David Pensak (thanks a lot, I,ve been trying to find this code unsuccessfully). I am sure there is other codes that can deal with those conformations of five-membered ring and generate a lot of them. Maybe I should formulate a different question to CC= L asking for this software (preferably free) All the best Reynier 2010/9/25 Patrick McCarren patrick.mccarren],[gmail.com < owner-chemistry .. ccl.net> > It sounds like the constraints are conflicting but the errors are not as > helpful as the input would be. Maybe you could provide your input file? = I > think this will be difficult to do using Gaussian alone. I would persona= lly > recommend just making each of the 20 fundamental ring conformers (E1, E2, > E3, E4, E5, 1E, 2E, 3E, 4E, 5E, 1T2, 2T1, etc. ) in a builder program, do= a > modredundant optimization with "D * * * * F" to fix all dihedrals at firs= t, > and then do an unfrozen optimization. You might have to gradually remove > restraints so you don't lose higher energy ring conformations if that's w= hat > you're trying to do. Another thing you could try is to use a conformatio= nal > search program with a ring-sampling algorithm. Spartan, MacroModel, MOE = are > a couple examples. You could put those structures in Gaussian, constrain > the ring dihedrals as above, optimize, and then reoptimize without > constraints. It depends on what you're trying to figure out though. > > Patrick > > > On Fri, Sep 24, 2010 at 3:27 PM, Reynier Suardiaz del R=EDo > reynier.suardiaz!^!gmail.com > > wrote: > >> 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 followin= g: I >> want to generate diferent conformations of this furanose ring by changin= g >> the dihedrals (between permitted values without breaking of the ring) an= d >> 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 angle= s, >> 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 i= s >>> that you typed something wrong. Notice that the program tried 99 itera= tions >>> to fit you frozen coordiate information into the optimization routine. >>> Either you connected the coordinates incorrectly, or did not have enoug= h >>> 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 ato= ms 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 enter t= he >>> 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 t= he >>> optimization routine bombs. >>> Regards, Dave Close. >>> >>> ________________________________________ >>> > From: owner-chemistry+closed=3D=3Detsu.edu[A]ccl.net[owner-chemistry+= closed=3D=3D >>> etsu.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 tr= y 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 partia= l >>> optimization in five-membered rings? Note that I can not freeze all the >>> dihedrals using optimization in internal coordinates (opt=3Dz-matrix wi= th 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/su= b_unsub.shtmlhttp://www.ccl.net/spammers.txt >>> >>> >>> -=3D This is automatically added to each message by the mailing script = =3D- >>> E-mail to subscribers: CHEMISTRY]*[ccl.net or use:>>> >>> E-mail to administrators: CHEMISTRY-REQUEST]*[ccl.net or use>>> >>> >>> >> >> >> -- >> reynier >> http://rincon.uam.es/dir?cw=3D331069946289062 >> > > --=20 reynier http://rincon.uam.es/dir?cw=3D331069946289062 --00c09f93d5db9e7aef04915158c5 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Patrick
Thanks a lot for your answer. The idea of using the main co= nformers sound very well but what I really would like to do is, besides tho= se conformers, generate much more at intermediate positions. What is really= happening is that I thought if I change the dihedrals in Gaussian using re= dundant coordinates, the software would change all dihedrals (without probl= ems because the combinations of dihedrals should be permitted) and performe= a partial optimization in this new conformation. After that, I would write= some simple code to automatically change the dihedrals to many permitted v= alues (to do that, I need the mathematical relation between dihedrals) and = to obtain many partially optimized conformations that I could use to calcul= ate properties. That plan does not work.... :-( 1st Gaussian can only perfo= rm the partial optimization if you freeze the dihedrals at the same value o= f the input geometry, if you change this values even to other geometrically= permitted combinations of dihedrals the calculations ends abnormally. 2nd = I do not have the mathematical relation between the dihedrals in order to c= hange one of them and predict the permitted values of the others. So I coul= d try to "play" with the geometries trying to find suitable combi= nations in some way as suggested by Pierre or David (many thanks to both) o= r I can look for a code to generate many conformers of a five membered ring= as PUCKER mentioned by David Pensak (thanks a lot, I,ve been trying to fin= d this code unsuccessfully). I am sure there is other codes that can deal w= ith those conformations of five-membered ring and generate a lot of them. M= aybe I should formulate a different question to CCL asking for this softwar= e (preferably free)
All the best
Reynier


2010/9/25 Patrick McCarren patrick.mccarren]= ,[gmail.com <owne= r-chemistry .. ccl.net>
It sounds like the constraints are conflicting but the errors are not as he= lpful as the input would be.=A0 Maybe you could provide your input file?=A0= I think this will be difficult to do using Gaussian alone.=A0 I would pers= onally recommend just making each of the 20 fundamental ring conformers (E1= , E2, E3, E4, E5, 1E, 2E, 3E, 4E, 5E, 1T2, 2T1, etc. ) in a builder program= , do a modredundant optimization with "D * * * * F" to fix all di= hedrals at first, and then do an unfrozen optimization.=A0 You might have t= o gradually remove restraints so you don't lose higher energy ring conf= ormations if that's what you're trying to do.=A0 Another thing you = could try is to use a conformational search program with a ring-sampling al= gorithm.=A0 Spartan, MacroModel, MOE are a couple examples.=A0 You could pu= t those structures in Gaussian, constrain the ring dihedrals as above, opti= mize, and then reoptimize without constraints.=A0 It depends on what you= 9;re trying to figure out though.=A0

Patrick


On Fri, = Sep 24, 2010 at 3:27 PM, Reynier Suardiaz del R=EDo reynier.suardiaz!^!gmail.com = <owner-= chemistry ~ ccl.net> wrote:
Dear D. Close
=
Many thanks for your answer, you was right. I typed the values of the d= ihedrals with 6 decimal places exactly matching with those of the input str= ucture. 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 di= hedrals (between permitted values without breaking of the ring) and partial= ly optimize this structures (obtained by slightly changing the dihedral val= ues) and keeping frozen the five dihedrals. When I try to do this using red= undant coordinates in gaussian I obtained the same error message than befor= e:

-------------
=A0Iteration 99 RMS(Cart)=3D=A0 0.00005822 RMS(Int)=3D= =A0 0.00955580
=A0Iteration100 RMS(Cart)=3D=A0 0.00005748 RMS(Int)=3D=A0= 0.00959825
=A0New curvilinear step not converged.
=A0Error imposing = constraints
=A0Error termination via Lnk1e in C:\G03W\l101.exe at Fri Se= p 24 21:05:06 2010.
=A0Job cpu time:=A0 0 days=A0 0 hours=A0 0 minutes=A0 1.0 seconds.
=A0Fi= le lengths (MBytes):=A0 RWF=3D=A0=A0=A0=A0=A0 7 Int=3D=A0=A0=A0=A0=A0 0 D2E= =3D=A0=A0=A0=A0=A0 0 Chk=3D=A0=A0=A0=A0=A0 8 Scr=3D=A0=A0=A0=A0=A0 1
---= -----------

even if I only change one dihedral from its original val= ue (at the input geometry) in less than one degree,=A0 the calculation ends= with the above error message.
Does anybody knows how to do this in gaussian, I mean, changing the dihedra= l angles of a five memebered ring (from its text input file) and to perform= e a partial geometrical optimization with diferent dihedral angles, other t= han the one of the input geometry?
any comment or suggestions are welcome.

thanks in advance and with v= ery best regards

Reynier


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

Sent to CCL by: "Close, David M." [CLOSED#,#mail.etsu.edu]
Reynier:
=A0There is no limit to how many dihedrals you can freeze. =A0The problem = is that you typed something wrong. =A0Notice that the program tried 99 iter= ations to fit you frozen coordiate information into the optimization routin= e.
Either you connected the coordinates incorrectly, or did not have enough pr= ecision in the frozen coordinate.
So if the input line has something like 10 5 6 8 =A0 31.3, first look at th= e string 10 5 6 8 and make sure this is correct. =A0The use a graphics prog= ram to examine the actual dihedral geometry. =A0Run through the 4 atoms in = the string 10 5 6 8 and see what the graphic program thinks the dihedral an= gle actually is. =A0Copy the value to 5-6 decimal places and re enter the d= ata.
=A0If this doesn't work, then you have to use trial and error. =A0You = said that freezing 2 dihedrals works. =A0But how many iterations did it tak= e? =A0I would expect only 2-3. =A0If more, then refine the coordinates, and= then add a third frozen dihedral. =A0You can quickly find the offending en= try when the optimization routine bombs.
=A0Regards, Dave Close.

________________________________________
> From: owner-chemistry+closed=3D=3Detsu.edu[A]ccl= .net [owner-chemistry+closed=3D=3Detsu.edu[A]ccl.ne= t] 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 =A0Suard =A0az" [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 o= f the input gaussian file the desired dihedrals to keep frozen. I am receiv= ing an error message when i try to keep frozen more than two dihedral angle= s (of the ring) at the same time. For example if I try to froze the five di= hedrals of the ring I get the following message:

------
=A0Iteration 99 RMS(Cart)=3D =A00.00001156 RMS(Int)=3D =A00.00309967
=A0Iteration100 RMS(Cart)=3D =A00.00001134 RMS(Int)=3D =A00.00310385
=A0New curvilinear step not converged.
=A0Error imposing constraints
=A0Error termination via Lnk1e in C:\G03W\l101.exe at Mon Sep 20 17:48:17 2= 010.
=A0Job cpu time: =A00 days =A00 hours =A00 minutes =A01.0 seconds.
=A0File lengths (MBytes): =A0RWF=3D =A0 =A0 =A07 Int=3D =A0 =A0 =A00 D2E=3D= =A0 =A0 =A00 Chk=3D =A0 =A0 =A07 Scr=3D =A0 =A0 =A01
---------

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 wit= h gaussian? Is there any other possibility to do this kind of partial optim= ization in five-membered rings? Note that I can not freeze all the dihedral= s using optimization in internal coordinates (opt=3Dz-matrix with a separat= e input section of "constants") because of to define a z-matrix o= f a five-membered ring are necesary only two dihedrals, so I have to use re= dundants.
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.c= cl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt



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




--
reynier
= http://rincon.uam.es/dir?cw=3D331069946289062
--00c09f93d5db9e7aef04915158c5-- From owner-chemistry@ccl.net Tue Sep 28 10:34:01 2010 From: "Jan Dillen jlmd|-|sun.ac.za" To: CCL Subject: CCL: Difference between IRC and minimization from TS Message-Id: <-42850-100928094558-21954-vgUmwcAApIXqHnRg+sWexA[A]server.ccl.net> X-Original-From: "Jan Dillen" Date: Tue, 28 Sep 2010 09:45:57 -0400 Sent to CCL by: "Jan Dillen" [jlmd-$-sun.ac.za] Could anyone explain whether there is a practical (in terms of results)difference in doing an IRC (in Cartesian coordinates) to find the two minima downhill from a transition state on the one hand, and doing a minimization of two structures that were distorted in opposite directions from the same TS using the eigenvector associated with the negative frequency on the other. I am not interested in the actual trajectory, only in establishing whether the TS is the correct one between the two minima. Jan From owner-chemistry@ccl.net Tue Sep 28 15:04:00 2010 From: "Juan C. Drosos jdrosos|*|gmail.com" To: CCL Subject: CCL:G: BSSE, COSMO and DFT Message-Id: <-42851-100928150227-23528-8P6nObCXv/bTxqoOoS+H7g%a%server.ccl.net> X-Original-From: "Juan C. Drosos" Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 28 Sep 2010 14:02:19 -0500 MIME-Version: 1.0 Sent to CCL by: "Juan C. Drosos" [jdrosos,+,gmail.com] Dear Sirs. We would like to know if it is correct to apply , during a G03 energy calculation (for a macromolecule-ligand system), the keywords BSSE (counterpoise) and COSMO (scrf=COSMO) at the same time?. We are concerned and confused because the trend in energies, when the system was considered <>, was excellent and in agreement with observed chemical phenomena. But once the solvation was included, the results significantly diverged and a total loss of chemical sense was observed. we used the functionals X3LYP and M06-2X with 6-311G(d,p) basis set. We would appreciate any comments. Best Regards. From owner-chemistry@ccl.net Tue Sep 28 20:10:00 2010 From: "Patrick McCarren patrick.mccarren]|[gmail.com" To: CCL Subject: CCL:G: freezen dihedrals in five-membered rings Message-Id: <-42852-100928170114-11506-bqt6tQbimxDN+2QR9EZrdg=server.ccl.net> X-Original-From: Patrick McCarren Content-Type: multipart/alternative; boundary=0016363ba7a079f2a104915824ec Date: Tue, 28 Sep 2010 17:01:01 -0400 MIME-Version: 1.0 Sent to CCL by: Patrick McCarren [patrick.mccarren**gmail.com] --0016363ba7a079f2a104915824ec Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable I don't have access to this paper but you might find some details or contac= t for obtaining a program for accomplishing this in the paper below. http://scripts.iucr.org/cgi-bin/paper?pn0051 Constructing rings of specified puckerR. P. Millaneand E. U. Nzewi *Abstract:* A method of constructing closed rings of specified pucker is described. A ring is constructed such that a set of puckering parameters as well as the ring bond lengths and bond angles are optimized towards desired values. A computer program is described which generates *N*-membered rings in this way and is illustrated with examples. Patrick On Tue, Sep 28, 2010 at 8:54 AM, Reynier Suardiaz del R=EDo reynier.suardiaz(a)gmail.com wrote: > Dear Patrick > Thanks a lot for your answer. The idea of using the main conformers sound > very well but what I really would like to do is, besides those conformers= , > generate much more at intermediate positions. What is really happening is > that I thought if I change the dihedrals in Gaussian using redundant > coordinates, the software would change all dihedrals (without problems > because the combinations of dihedrals should be permitted) and performe a > partial optimization in this new conformation. After that, I would write > some simple code to automatically change the dihedrals to many permitted > values (to do that, I need the mathematical relation between dihedrals) a= nd > to obtain many partially optimized conformations that I could use to > calculate properties. That plan does not work.... :-( 1st Gaussian can on= ly > perform the partial optimization if you freeze the dihedrals at the same > value of the input geometry, if you change this values even to other > geometrically permitted combinations of dihedrals the calculations ends > abnormally. 2nd I do not have the mathematical relation between the > dihedrals in order to change one of them and predict the permitted values= of > the others. So I could try to "play" with the geometries trying to find > suitable combinations in some way as suggested by Pierre or David (many > thanks to both) or I can look for a code to generate many conformers of a > five membered ring as PUCKER mentioned by David Pensak (thanks a lot, I,v= e > been trying to find this code unsuccessfully). I am sure there is other > codes that can deal with those conformations of five-membered ring and > generate a lot of them. Maybe I should formulate a different question to = CCL > asking for this software (preferably free) > All the best > Reynier > > > 2010/9/25 Patrick McCarren patrick.mccarren],[gmail.com ~~ ccl.net > > >> It sounds like the constraints are conflicting but the errors are not as >> helpful as the input would be. Maybe you could provide your input file?= I >> think this will be difficult to do using Gaussian alone. I would person= ally >> recommend just making each of the 20 fundamental ring conformers (E1, E2= , >> E3, E4, E5, 1E, 2E, 3E, 4E, 5E, 1T2, 2T1, etc. ) in a builder program, d= o a >> modredundant optimization with "D * * * * F" to fix all dihedrals at fir= st, >> and then do an unfrozen optimization. You might have to gradually remov= e >> restraints so you don't lose higher energy ring conformations if that's = what >> you're trying to do. Another thing you could try is to use a conformati= onal >> search program with a ring-sampling algorithm. Spartan, MacroModel, MOE= are >> a couple examples. You could put those structures in Gaussian, constrai= n >> the ring dihedrals as above, optimize, and then reoptimize without >> constraints. It depends on what you're trying to figure out though. >> >> Patrick >> >> >> On Fri, Sep 24, 2010 at 3:27 PM, Reynier Suardiaz del R=EDo >> reynier.suardiaz!^!gmail.com >> > wrote: >> >>> 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 inpu= t >>> structure. Doing this, the geometry optimization have finished without >>> problem in a few iterations. Now what I would like to do is the followi= ng: I >>> want to generate diferent conformations of this furanose ring by changi= ng >>> the dihedrals (between permitted values without breaking of the ring) a= nd >>> partially optimize this structures (obtained by slightly changing the >>> dihedral values) and keeping frozen the five dihedrals. When I try to d= o >>> 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 inpu= t >>> 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 angl= es, >>> 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 iter= ations >>>> to fit you frozen coordiate information into the optimization routine. >>>> Either you connected the coordinates incorrectly, or did not have enou= gh >>>> 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 at= oms in >>>> the string 10 5 6 8 and see what the graphic program thinks the dihedr= al >>>> 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=3D >>>> etsu.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 th= e >>>> 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 t= ry 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 17:48:1= 7 >>>> 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 proble= m >>>> with gaussian? Is there any other possibility to do this kind of parti= al >>>> optimization in five-membered rings? Note that I can not freeze all th= e >>>> dihedrals using optimization in internal coordinates (opt=3Dz-matrix w= ith 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/s= ub_unsub.shtmlhttp://www.ccl.net/spammers.txt >>>> >>>> >>>> -=3D This is automatically added to each message by the mailing script= =3D- >>>> E-mail to subscribers: CHEMISTRY]*[ccl.net or use:>>>> >>>> E-mail to administrators: CHEMISTRY-REQUEST]*[ccl.net or use>>>> Conferences: http://server.ccl.net/chemistry/announcements/conferences= />>>> >>>> >>>> >>> >>> >>> -- >>> reynier >>> http://rincon.uam.es/dir?cw=3D331069946289062 >>> >> >> > > > -- > reynier > http://rincon.uam.es/dir?cw=3D331069946289062 > --0016363ba7a079f2a104915824ec Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable I don't have access to this paper but you might find some details or co= ntact for obtaining a program for accomplishing this in the paper below.=A0=

Constructing rings of specified puck= er

R. P. Millane and E. U. Nzewi

Abstract: A metho= d of constructing closed=20 rings of specified pucker is described. A ring is constructed such that a set of puckering parameters as well as the ring bond lengths and bond=20 angles are optimized towards desired values. A computer program is=20 described which generates N-membered=20 rings in this way and is illustrated with examples.


Patrick

<= div class=3D"gmail_quote">On Tue, Sep 28, 2010 at 8:54 AM, Reynier Suardiaz= del R=EDo reynier.suardiaz(a)gmail.com <owner-chemis= try^^^ccl.net> wrote:
Dear Patrick
T= hanks a lot for your answer. The idea of using the main conformers sound ve= ry well but what I really would like to do is, besides those conformers, ge= nerate much more at intermediate positions. What is really happening is tha= t I thought if I change the dihedrals in Gaussian using redundant coordinat= es, the software would change all dihedrals (without problems because the c= ombinations of dihedrals should be permitted) and performe a partial optimi= zation in this new conformation. After that, I would write some simple code= to automatically change the dihedrals to many permitted values (to do that= , I need the mathematical relation between dihedrals) and to obtain many pa= rtially optimized conformations that I could use to calculate properties. T= hat plan does not work.... :-( 1st Gaussian can only perform the partial op= timization if you freeze the dihedrals at the same value of the input geome= try, if you change this values even to other geometrically permitted combin= ations of dihedrals the calculations ends abnormally. 2nd I do not have the= mathematical relation between the dihedrals in order to change one of them= and predict the permitted values of the others. So I could try to "pl= ay" with the geometries trying to find suitable combinations in some w= ay as suggested by Pierre or David (many thanks to both) or I can look for = a code to generate many conformers of a five membered ring as PUCKER mentio= ned by David Pensak (thanks a lot, I,ve been trying to find this code unsuc= cessfully). I am sure there is other codes that can deal with those conform= ations of five-membered ring and generate a lot of them. Maybe I should for= mulate a different question to CCL asking for this software (preferably fre= e)
All the best
Reynier


2010/9/25 Patrick McCarren patrick.mccarren]= ,[gmail.com <owner-chemistry ~~ ccl.net>
It sounds like the constraints are conflicting but the errors are not as he= lpful as the input would be.=A0 Maybe you could provide your input file?=A0= I think this will be difficult to do using Gaussian alone.=A0 I would pers= onally recommend just making each of the 20 fundamental ring conformers (E1= , E2, E3, E4, E5, 1E, 2E, 3E, 4E, 5E, 1T2, 2T1, etc. ) in a builder program= , do a modredundant optimization with "D * * * * F" to fix all di= hedrals at first, and then do an unfrozen optimization.=A0 You might have t= o gradually remove restraints so you don't lose higher energy ring conf= ormations if that's what you're trying to do.=A0 Another thing you = could try is to use a conformational search program with a ring-sampling al= gorithm.=A0 Spartan, MacroModel, MOE are a couple examples.=A0 You could pu= t those structures in Gaussian, constrain the ring dihedrals as above, opti= mize, and then reoptimize without constraints.=A0 It depends on what you= 9;re trying to figure out though.=A0

Patrick


On Fri, = Sep 24, 2010 at 3:27 PM, Reynier Suardiaz del R=EDo reynier.suardiaz!^!gmail.com = <owner-= chemistry ~ ccl.net> wrote:
Dear D. Close
=
Many thanks for your answer, you was right. I typed the values of the d= ihedrals with 6 decimal places exactly matching with those of the input str= ucture. 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 di= hedrals (between permitted values without breaking of the ring) and partial= ly optimize this structures (obtained by slightly changing the dihedral val= ues) and keeping frozen the five dihedrals. When I try to do this using red= undant coordinates in gaussian I obtained the same error message than befor= e:

-------------
=A0Iteration 99 RMS(Cart)=3D=A0 0.00005822 RMS(Int)=3D= =A0 0.00955580
=A0Iteration100 RMS(Cart)=3D=A0 0.00005748 RMS(Int)=3D=A0= 0.00959825
=A0New curvilinear step not converged.
=A0Error imposing = constraints
=A0Error termination via Lnk1e in C:\G03W\l101.exe at Fri Se= p 24 21:05:06 2010.
=A0Job cpu time:=A0 0 days=A0 0 hours=A0 0 minutes=A0 1.0 seconds.
=A0Fi= le lengths (MBytes):=A0 RWF=3D=A0=A0=A0=A0=A0 7 Int=3D=A0=A0=A0=A0=A0 0 D2E= =3D=A0=A0=A0=A0=A0 0 Chk=3D=A0=A0=A0=A0=A0 8 Scr=3D=A0=A0=A0=A0=A0 1
---= -----------

even if I only change one dihedral from its original val= ue (at the input geometry) in less than one degree,=A0 the calculation ends= with the above error message.
Does anybody knows how to do this in gaussian, I mean, changing the dihedra= l angles of a five memebered ring (from its text input file) and to perform= e a partial geometrical optimization with diferent dihedral angles, other t= han the one of the input geometry?
any comment or suggestions are welcome.

thanks in advance and with v= ery best regards

Reynier


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

Sent to CCL by: "Close, David M." [CLOSED#,#mail.etsu.edu]
Reynier:
=A0There is no limit to how many dihedrals you can freeze. =A0The problem = is that you typed something wrong. =A0Notice that the program tried 99 iter= ations to fit you frozen coordiate information into the optimization routin= e.
Either you connected the coordinates incorrectly, or did not have enough pr= ecision in the frozen coordinate.
So if the input line has something like 10 5 6 8 =A0 31.3, first look at th= e string 10 5 6 8 and make sure this is correct. =A0The use a graphics prog= ram to examine the actual dihedral geometry. =A0Run through the 4 atoms in = the string 10 5 6 8 and see what the graphic program thinks the dihedral an= gle actually is. =A0Copy the value to 5-6 decimal places and re enter the d= ata.
=A0If this doesn't work, then you have to use trial and error. =A0You = said that freezing 2 dihedrals works. =A0But how many iterations did it tak= e? =A0I would expect only 2-3. =A0If more, then refine the coordinates, and= then add a third frozen dihedral. =A0You can quickly find the offending en= try when the optimization routine bombs.
=A0Regards, Dave Close.

________________________________________
> From: owner-chemistry+closed=3D=3Detsu.edu[A]ccl= .net [owner-chemistry+closed=3D=3Detsu.edu[A]ccl.ne= t] 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 =A0Suard =A0az" [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 o= f the input gaussian file the desired dihedrals to keep frozen. I am receiv= ing an error message when i try to keep frozen more than two dihedral angle= s (of the ring) at the same time. For example if I try to froze the five di= hedrals of the ring I get the following message:

------
=A0Iteration 99 RMS(Cart)=3D =A00.00001156 RMS(Int)=3D =A00.00309967
=A0Iteration100 RMS(Cart)=3D =A00.00001134 RMS(Int)=3D =A00.00310385
=A0New curvilinear step not converged.
=A0Error imposing constraints
=A0Error termination via Lnk1e in C:\G03W\l101.exe at Mon Sep 20 17:48:17 2= 010.
=A0Job cpu time: =A00 days =A00 hours =A00 minutes =A01.0 seconds.
=A0File lengths (MBytes): =A0RWF=3D =A0 =A0 =A07 Int=3D =A0 =A0 =A00 D2E=3D= =A0 =A0 =A00 Chk=3D =A0 =A0 =A07 Scr=3D =A0 =A0 =A01
---------

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 wit= h gaussian? Is there any other possibility to do this kind of partial optim= ization in five-membered rings? Note that I can not freeze all the dihedral= s using optimization in internal coordinates (opt=3Dz-matrix with a separat= e input section of "constants") because of to define a z-matrix o= f a five-membered ring are necesary only two dihedrals, so I have to use re= dundants.
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.c= cl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt



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




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

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