From owner-chemistry@ccl.net Sat Oct 18 02:46:01 2008 From: "Raphael Ribeiro raphaelri_-_hotmail.com" To: CCL Subject: CCL: Potentials of Mean Force and continuum solvation models Message-Id: <-37943-081018022342-14447-GCUcejhP4Bz0gSj/ofO6Tw~!~server.ccl.net> X-Original-From: "Raphael Ribeiro" Date: Sat, 18 Oct 2008 02:23:38 -0400 Sent to CCL by: "Raphael Ribeiro" [raphaelri ~ hotmail.com] Dear all, I have recently read in Cramer's "Essentials of Computational Chemistry" that potentials of mean force are not well described in continuum solvent models(CSM) (which was already expected by me), however he says that that CSM models that use cavity-based approach to solve Poisson equation are especially not good for solving the related equations and then he explains by talking about numerical instabilities because then we have two cavities instead of one (the solute's cavity). What would be this other cavity? A cavity related to solvent? Also, he says Generalized Born models do not suffer from this problem, but even though they are not succesful in predicting this kind of data. I can imagine why the GB equation is less affected by the introduction of another cavity, but I would like to have some more specific information on how CSM deals with potentials of mean force. I've looked at the references in Cramer's book but they were not what I was looking for. Any comments would be appreciated. Thanks in advance Raphael Ribeiro From owner-chemistry@ccl.net Sat Oct 18 11:44:00 2008 From: "Carlos Alberto Franca carfranca120(-)gmail.com" To: CCL Subject: CCL: molecular modeling of copper (II) coordination complex Message-Id: <-37944-081018104627-2569-212JmnH0TzufYRRwBEyN/A||server.ccl.net> X-Original-From: "Carlos Alberto Franca" Content-Type: multipart/alternative; boundary="----=_Part_86880_11817962.1224341176943" Date: Sat, 18 Oct 2008 11:46:16 -0300 MIME-Version: 1.0 Sent to CCL by: "Carlos Alberto Franca" [carfranca120]-[gmail.com] ------=_Part_86880_11817962.1224341176943 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline arthur I constucted a cu complex using Hyperchem software and had no problems in do that. the bonds cu-ligand may be considered as covalents ------=_Part_86880_11817962.1224341176943 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
arthur
I constucted a cu complex using Hyperchem software and had no problems in do that.
the bonds cu-ligand may be considered as covalents
------=_Part_86880_11817962.1224341176943-- From owner-chemistry@ccl.net Sat Oct 18 12:19:00 2008 From: "Carlos Alberto Franca carfranca120#%#gmail.com" To: CCL Subject: CCL: molecular modeling of copper (II) coordination complex Message-Id: <-37945-081018103410-949-dEZ8JbAsKzHKf6jXauTNHA(-)server.ccl.net> X-Original-From: "Carlos Alberto Franca" Content-Type: multipart/alternative; boundary="----=_Part_86852_32180493.1224340437689" Date: Sat, 18 Oct 2008 11:33:57 -0300 MIME-Version: 1.0 Sent to CCL by: "Carlos Alberto Franca" [carfranca120|*|gmail.com] ------=_Part_86852_32180493.1224340437689 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline arthur I constucted a cu complex using Hyperchem software and had no problems in do that. the bonds cu-ligand may be considered as covalents 2008/10/17 Arthur computationalboy]=[gmail.com > Dear all: > I have problems in modeling coordination complex such as copper (II)- His > complex for conformational analysis and global lowest energy computation. > Can anyone give me some instructions on how to consider the coordination > bonds? I cannot construct the complex structure in Sybyl (Tripos) since the > software allways considers the bonds as covalent. > Any suggestion would be greatly appreciated. > > Yours sincerely Arthur > -- > Arthur J. Wang > Shenyang Pharmaceutical University P.O. Box 40 > 103 Wenhua Road, Shenhe District > Shenyang,110016, P. R. China > Tel : +86 24 23986419 > Fax: +86 24 23995043 > E-Mail: wjmed(at)126.com ; > computationalboy(at)gmail.com ------=_Part_86852_32180493.1224340437689 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
arthur
I constucted a cu complex using Hyperchem software and had no problems in do that.
the bonds cu-ligand may be considered as covalents
 


 
2008/10/17 Arthur computationalboy]=[gmail.com <owner-chemistry:_:ccl.net>
Dear all:
I have problems in modeling coordination complex such as copper (II)- His complex for conformational analysis and global lowest energy computation.  Can anyone give me some instructions on how to consider the coordination bonds? I cannot construct the complex structure in Sybyl (Tripos) since the software allways considers the bonds as covalent.
Any suggestion would be greatly appreciated.

Yours sincerely Arthur
--
Arthur J. Wang
Shenyang Pharmaceutical University P.O. Box 40
103 Wenhua Road, Shenhe District
Shenyang,110016, P. R. China
Tel : +86 24 23986419
Fax: +86 24 23995043
E-Mail:  wjmed(at)126.com ;
      computationalboy(at)gmail.com

------=_Part_86852_32180493.1224340437689-- From owner-chemistry@ccl.net Sat Oct 18 15:47:00 2008 From: "Tuhin Kumar Pal tuhin%iitk.ac.in" To: CCL Subject: CCL:G: Unable to project occupied orbitals ! Message-Id: <-37946-081018123902-18440-7jq+J5JjBhj9qQY+IcucEw__server.ccl.net> X-Original-From: "Tuhin Kumar Pal" Date: Sat, 18 Oct 2008 12:38:58 -0400 Sent to CCL by: "Tuhin Kumar Pal" [tuhin++iitk.ac.in] Dear CCL users, I'm very new to QM, hopefully 3 months. I submitted a job to calculate the corrected interaction energy between subunit:A and B of a complex:AB using Counterpoised (CP) method. This is what the command is: %chk=file_check %rwf=a1, 1gb, a2, 1gb, a3, 1gb, a4, 1gb, a5, 1gb, a6, 1gb, a7, 1gb, a8, 1gb, a9, 1gb, a10, 1gb, a11, 1gb, a12, 1gb, a13, 1gb, a14, 1gb, a15, 1gb, a16, 1gb, a17, 1gb, a18, 1gb, a193, 1gb, a20, -1 #MP2/6-31++G** SCF=(MaxCycle=999) Counterpoise=2 But, the calculation terminates in an ERROR stating: Unable to project occupied orbitals ! Error termination via Lnk1e in /home/rsankar/alok/gaussion/g03/l401.exe at Mon Oct 13 10:50:04 2008. Job cpu time: 4 days 3 hours 21 minutes 51.6 seconds. File lengths (MBytes): RWF= 13241 Int= 0 D2E= 0 Chk= 16 Scr= 1 Could anybody let me know, what am I doing wrong? Waiting for your suggestions. Thanks in advance. Best regards, Tuhin NB: I search the archive but I ended-up getting the questions with same ERROR but no answers/remedies. From owner-chemistry@ccl.net Sat Oct 18 23:23:00 2008 From: "Bruno Andrade bandradefsa[#]yahoo.com.br" To: CCL Subject: CCL: Problems in protein modeling Message-Id: <-37947-081018222746-31814-kt2YMBDyE0MtFOL8fZ67Ng|server.ccl.net> X-Original-From: "Bruno Andrade" Date: Sat, 18 Oct 2008 22:27:41 -0400 Sent to CCL by: "Bruno Andrade" [bandradefsa^^yahoo.com.br] Hi people! I have been working with protein homology modeling, but now I a have a protein sequence wich have a very low identity with other proteins deposited in the PDB and other database (very high e-value, and low score, too). When I submit my protein to an homology modeling process, the result is very bad... the program returns to a small part of this molecule modeled. So, I thougth someone can help in another kind of molecular modeling, such ab initio, and as I can solve me protein structure. If you know something about any free program or tool on the internet, it will be very helpfull to my work. Thank you very much. Bruno Andrade. From owner-chemistry@ccl.net Sat Oct 18 23:58:01 2008 From: "Arthur computationalboy^_^gmail.com" To: CCL Subject: CCL: molecular modeling of copper (II) coordination complex Message-Id: <-37948-081018234457-23192-2k3YdQJGeRjduStzc+k4gQ(a)server.ccl.net> X-Original-From: Arthur Content-Type: multipart/alternative; boundary="----=_Part_42314_17801217.1224387886521" Date: Sun, 19 Oct 2008 11:44:46 +0800 MIME-Version: 1.0 Sent to CCL by: Arthur [computationalboy~~gmail.com] ------=_Part_42314_17801217.1224387886521 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Thank you for your kind reply! I dis consider the coordiantion bond in a copper complex with pyridine as covalent bond, however, the atom type of nitrogen atom changed from N.ar to N.4 and the pyridine ring cannot maintain plane. I think it was incorrect. Therefore, there must be a methond for considering coordiantion bond other than covalent bond in coordination complex. Thanks! On 10/18/08, Carlos Alberto Franca carfranca120(-)gmail.com < owner-chemistry[#]ccl.net> wrote: > > arthur > I constucted a cu complex using Hyperchem software and had no problems in > do that. > the bonds cu-ligand may be considered as covalents > -- Arthur J. Wang Shenyang Pharmaceutical University P.O. Box 40 103 Wenhua Road, Shenhe District Shenyang,110016, P. R. China Tel : +86 24 23986419 Fax: +86 24 23995043 E-Mail: wjmed(at)126.com ; computationalboy(at)gmail.com ------=_Part_42314_17801217.1224387886521 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Thank you for your kind reply!
I dis consider the coordiantion bond in a copper complex with pyridine as covalent bond, however, the atom type of nitrogen atom changed from N.ar to N.4 and the pyridine ring cannot maintain plane. I think it was incorrect. Therefore, there must be a methond for considering coordiantion bond other than covalent bond in coordination complex.
Thanks!
 
On 10/18/08, Carlos Alberto Franca carfranca120(-)gmail.com <owner-chemistry[#]ccl.net> wrote:
arthur
I constucted a cu complex using Hyperchem software and had no problems in do that.
the bonds cu-ligand may be considered as covalents



--
Arthur J. Wang
Shenyang Pharmaceutical University P.O. Box 40
103 Wenhua Road, Shenhe District
Shenyang,110016, P. R. China
Tel : +86 24 23986419
Fax: +86 24 23995043
E-Mail:  wjmed(at)126.com ;
      computationalboy(at)gmail.com ------=_Part_42314_17801217.1224387886521--