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.=A0 To see this, consider a special case where all the atoms li= e in a plane.=A0 All five dihedral angles equal 0.=A0 If you constrain all = five angles to be zero, Gaussian is happy to optimize this.=A0 Now suppose = you change one of the angles, even if you only change it to +1 degree.=A0 I= t becomes geometrically IMPOSSIBLE.=A0 Because four of the five dihedrals a= re still zero, all five atoms are still forced to lie in a single plane.=A0= Then a mathematical consequence is that the fifth dihedral is automaticall= y zero also.=A0 If you tell it to make that dihedral equal to +1, you are a= sking Gaussian to find a geometry that mathematically cannot exist.=A0 Gues= s what: Gaussian cannot do it, and gives you an error message.=A0 The error= message is appropriate: "error imposing constraints".

If you want to change one dihedral angle a little, you must allow some of t= he other four dihedral angles to adapt to the change.=A0 If you work a litt= le 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 an= gles are also fixed, but it is hard to adapt bond lengths and angles to acc= ommodate changing dihedral angles.)=A0 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.=A0 I think Gaussian wi= ll be happy with that and will be able to converge.=A0 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.=A0 I= f 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 -id#3= te-" <davi= d.anick\a/rcn.com>

Dear D. Close

Many thanks for your answer, you was right. I typed the values of the dihed= rals with 6 decimal places exactly matching with those of the input structu= re. 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 g= enerate diferent conformations of this furanose ring by changing the dihedr= als (between permitted values without breaking of the ring) and partially o= ptimize this structures (obtained by slightly changing the dihedral values)= and keeping frozen the five dihedrals. When I try to do this using redunda= nt coordinates in gaussian I obtained the same error message than before:
-------------
=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 Sep 24 21:05:06 2= 010.
=A0Job cpu time:=A0 0 days=A0 0 hours=A0 0 minutes=A0 1.0 seconds.
=A0File 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 value (at the input ge= ometry) in less than one degree,=A0 the calculation ends with the above err= or message.
Does anybody knows how to do this in gaussian, I mean, chang= ing 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

20= 10/9/22 Close, David M. CLOSED~!~mail.etsu.edu <owner-chemistry]*[ccl.net><= /span>

=

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.
=A0Fi= le 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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http://rincon.uam.es/dir?cw=3D331069946289062

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.n= et/chemistry/sub_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:
http://www.ccl.net/cgi-bin/ccl/send_ccl_message

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