From owner-chemistry@ccl.net Thu Aug 30 01:20:00 2012 From: "Ivanciuc, Ovidiu I. oiivanci_+_utmb.edu" To: CCL Subject: CCL: Topological descriptor of 'molecular length' Message-Id: <-47502-120830011831-1784-AYvsoL/LYXZJFtwM9modyA[-]server.ccl.net> X-Original-From: "Ivanciuc, Ovidiu I." Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 30 Aug 2012 05:18:02 +0000 MIME-Version: 1.0 Sent to CCL by: "Ivanciuc, Ovidiu I." [oiivanci#%#utmb.edu] Joaquin, The STERMIOL parameters are a measure of the size of a substituent or a molecule; see here for a FORTRAN code: http://www.ccl.net/cca/software/SOURCES/FORTRAN/STERIMOL/ Another geometric parameter to consider is ovality, available in Cerius2, for example. For a QSAR-like approach, you might try molecular moments - see the papers on Comparative Molecular Moment Analysis (CoMMA). O ________________________________________ > From: owner-chemistry+oiivanci==utmb.edu(-)ccl.net [owner-chemistry+oiivanci==utmb.edu(-)ccl.net] on behalf of Joaquin Barroso Flores joaco_barroso_-_yahoo.com [owner-chemistry(-)ccl.net] Sent: Wednesday, August 29, 2012 4:44 PM To: Ivanciuc, Ovidiu I. Subject: CCL: Topological descriptor of 'molecular length' Dear CCLers, Is anybody aware if there is a molecular descriptor of the molecular length/shape and the proper software to calculate it? I'd like to find a way to systematically treat rod-shaped or rod-like shaped molecules as a simple vector (with arbitrary direction imposed systematically under a suitable criterion) in order to have a shape-size descriptor of these molecules. Thanks in advanced for any help provided to this question. Greetings from Mexico ======================================================= Joaquin Barroso-Flores, Ph. D. Centro Conjunto de Investigacion en Quimica Sustentable Instituto de Quimica UNAM -> http://joaquinbarroso.wordpress.com joaquin.barroso''a''gmail.com "Blogastronomía": http://joaquinbarroso.blogspot.com ======================================================= From owner-chemistry@ccl.net Thu Aug 30 05:55:00 2012 From: "Julianna Olah olahjulcsi(~)freemail.hu" To: CCL Subject: CCL:G: ONIOM and UFF force field, question regarding MM charges Message-Id: <-47503-120830053152-23693-giWUCTk6E8jPt53X4PjtiQ^server.ccl.net> X-Original-From: "Julianna Olah" Date: Thu, 30 Aug 2012 05:31:51 -0400 Sent to CCL by: "Julianna Olah" [olahjulcsi#,#freemail.hu] Dear Computational Chemists, I would like to ask your help regarding ONIOM. I have used Gaussian for a rather long time, but I have just decided to do some ONIOM calculations and I have a few problems that I could not figure out from the manual. I am trying to do an (B3LYP/6-31G*:UFF) ONIOM calculation with embedded charges on a 3water + chloride ion system, where one water molecule is in the High layer and the rest in the lower layer. The calculations do seem to run, however, the sanity checks seem to indicate to me that the program does something else then what I expected. Here is my input: # oniom(B3LYP/6-31G*:UFF)=EmbedCharge geom=connectivity opt first trial -1 1 0 1 0 1 O -5.70826304 1.18887013 0.00000000 L H -4.74826304 1.18887013 0.00000000 L H -6.02871763 2.09380597 0.00000000 L O -2.90918477 1.39123101 0.03580473 H H -1.94918477 1.39123101 0.03580473 H H -3.22963936 2.29616684 0.03580473 H O -0.16188832 1.53559407 -0.26859314 L H 0.79811168 1.53559407 -0.26859314 L H -0.48234291 2.44052990 -0.26859314 L Cl -2.76020831 -1.16476536 0.04974641 L 1 2 1.0 3 1.0 2 3 4 5 1.0 6 1.0 5 6 7 8 1.0 9 1.0 8 9 10 When the calculation starts to run the MM sanity check says: MM sanity checks: All charges sum to: 0.00000000 Charges of atoms sum to: 0.00000000 Layer 1 (S) has 3 atoms and charge 0.00000000 sum= 0.00000000 Layer 2 (R) adds 7 atoms and charge 0.00000000 sum= 0.00000000 This tells me that assignemnt of charges is not what I expected, and that there is no charge on the MM region despite the fact that in the input file I indicated a -1 charge for the real system (and which is acknowledged by the program in the output file as well.) When I constructed my input file I relied on the gaussian manual which said that "The molecule specification includes atom types (which are optional with UFF but required by Amber)." so I kind of expected that somehow the program would know I wanted to have a chloride ion,but apparently I am mistaken. I tried to do a similar calculation starting from a protein pdb which contained ionized residues and for them using the same methodology, the charge of a glutamate residue was also said to be 0 instead of -1. I read the original Rapp et al paper on the UFF force field (JACS, 1992, 114, 10024), and there in Table 1 I see that each atom type has an effective charge. My questionS are: are these effective charges taken into account in Gaussian ONIOM calculations when UFF force field is used or not? If yes, what do I need to do have a proper charge distribution in the MM region? e.g. that a charged glutamate would have a -1 charge? or UFF can only be used with mechanical embedding and AMBER with both mechanical and electrostatic embedding? Could someone, please, advise me a good program to convert a charmm pdb file to amber pdb file to have proper amber atom types? thank you for your help in advance, Julianna Olah Dr. Julianna Olh Senior Research Fellow HAS-BME Materials Structure and Modeling Research Group Budapest University of Technology and Economics H-1111 Budapest, Gellrt tr 4. Hungary tel: (00)36/1-4632278 http://www.amkcs.ch.bme.hu/JO/index.html From owner-chemistry@ccl.net Thu Aug 30 08:20:01 2012 From: "psavita savita.pundlik+/-crl-global.com" To: CCL Subject: CCL: Topological descriptor of 'molecular length' Message-Id: <-47504-120830010036-761-RTWxw7q8FNT35FuiFi2jsw]_[server.ccl.net> X-Original-From: psavita Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 Date: Thu, 30 Aug 2012 10:30:23 +0530 MIME-Version: 1.0 Sent to CCL by: psavita [savita.pundlik-$-crl-global.com] Hello,

For neutral species, I have often seen the use of atom= ic covalent or vdW radii used for generating the molecular surface (its ext= ent).
For anions, the so-called minimal surface was found to be a very g= ood descriptor of the molecular shape and size. Kindly refer to
the work= s of S.R. Gadre and coworkers in the 80's or 90's.

Good luck and Re= gards,

S= avita Pundlik
Computational Materials Research & Innovation Group
Computati= onal Research Laboratories Ltd.,
Taco Hou= se, Damle Path, Off Law College Road
Pune - 411004, India.




-----owner-chemistry+savita.= pundlik=3D=3Dcrl-global.com_+_ccl.net wrote: -----
To: "Pundlik, Savita Sunil " <savit= a.pundlik_+_crl-global.com>
From: "Joaquin Barroso Flores joaco=5Fb= arroso=5F-=5Fyahoo.com"
Sent by: owner-chemistry+savita.pundlik=3D=3Dcrl-global.c= om_+_ccl.net
Date: 08/30/2012 04:16AM
Subject: CCL: Topological des= criptor of 'molecular length'

Dear CCLers,

Is anybody aware if the= re is a molecular descriptor of the molecular length/shape and the proper s= oftware to calculate it?
I'd like to find a way to systematically treat = rod-shaped or rod-like shaped molecules as a simple vector (with arbitrary = direction imposed systematically under a suitable criterion) in order to ha= ve a shape-size descriptor of these molecules.

Thanks in advanced fo= r any help provided to this question.

Greetings from Mexico
&nb= sp;
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Joaquin Barroso-Flores, Ph. D.
Centro = Conjunto de Investigacion en Quimica Sustentable
Instituto de QuimicaUNAM



joaquin.barroso''a''gmail.com


"Blogas= tronom=EDa":=0D http://joaquinbarroso.blogspot.com
=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D
= From owner-chemistry@ccl.net Thu Aug 30 09:07:00 2012 From: "Michel Petitjean petitjean.chiral!A!gmail.com" To: CCL Subject: CCL: Topological descriptor of 'molecular length' Message-Id: <-47505-120830090434-2499-/JfyXly3izeHuSu+D+8JXA]-[server.ccl.net> X-Original-From: Michel Petitjean Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 30 Aug 2012 15:04:22 +0200 MIME-Version: 1.0 Sent to CCL by: Michel Petitjean [petitjean.chiral,gmail.com] Dear Joaquin, There are several "lengths": 1. The diameter D, i.e. the distance between the two atoms the farthest one from the other, i.e. the length of the longest atom-pair 2. The diameter 2R of the smallest sphere enclosing the molecule, i.e. twice the radius R of this sphere. CARE: D may differ from 2R. 3. The smallest size H, i.e. the distance between the two closest parallel planes (slabs) enclosing the molecule. All these parameters are computed by the freeware RADI: see at the bottom of the page http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html Best regards, Michel. 2012/8/29 Joaquin Barroso Flores joaco_barroso_-_yahoo.com : > Dear CCLers, > > Is anybody aware if there is a molecular descriptor of the molecular > length/shape and the proper software to calculate it? > I'd like to find a way to systematically treat rod-shaped or rod-like shaped > molecules as a simple vector (with arbitrary direction imposed > systematically under a suitable criterion) in order to have a shape-size > descriptor of these molecules. > > Thanks in advanced for any help provided to this question. > > Greetings from Mexico > > ======================================================= > Joaquin Barroso-Flores, Ph. D. > Centro Conjunto de Investigacion en Quimica Sustentable > Instituto de Quimica > UNAM > > -> http://joaquinbarroso.wordpress.com > > > joaquin.barroso''a''gmail.com > > > "Blogastronomía": http://joaquinbarroso.blogspot.com > ======================================================= From owner-chemistry@ccl.net Thu Aug 30 09:42:00 2012 From: "Wolf Ihlenfeldt wdi#%#xemistry.com" To: CCL Subject: CCL: Topological descriptor of 'molecular length' Message-Id: <-47506-120830090941-5233-mnMnXCVRSL761vubJmvm3w*server.ccl.net> X-Original-From: Wolf Ihlenfeldt Content-Type: multipart/alternative; boundary=20cf307810f48ca87704c87b628a Date: Thu, 30 Aug 2012 15:09:26 +0200 MIME-Version: 1.0 Sent to CCL by: Wolf Ihlenfeldt [wdi%xemistry.com] --20cf307810f48ca87704c87b628a Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable I'd say the simplest descriptors meeting your requirement are the principal moments of intertia, or in your case, the ratio between them. They are trivial to compute (just Eigenvectors of the atomic coords). On Wed, Aug 29, 2012 at 11:44 PM, Joaquin Barroso Flores joaco_barroso_-_yahoo.com wrote: > Dear CCLers, > > Is anybody aware if there is a molecular descriptor of the molecular > length/shape and the proper software to calculate it? > I'd like to find a way to systematically treat rod-shaped or rod-like > shaped molecules as a simple vector (with arbitrary direction imposed > systematically under a suitable criterion) in order to have a shape-size > descriptor of these molecules. > > Thanks in advanced for any help provided to this question. > > Greetings from Mexico > > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D > Joaquin Barroso-Flores, Ph. D. > Centro Conjunto de Investigacion en Quimica Sustentable > Instituto de Quimica > UNAM > > -> http://joaquinbarroso.wordpress.com > > > joaquin.barroso''a''gmail.com > > > "Blogastronom=C3=ADa": http://joaquinbarroso.blogspot.com > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D > --=20 Wolf-D. Ihlenfeldt - Xemistry GmbH - wdi _ xemistry.com Phone: +49 6174 201455 - Fax +49 6174 209665 --- xemistry gmbh =E2=80=93 Gesch=C3=A4ftsf=C3=BChrer/Managing Director: Dr. W.= D. Ihlenfeldt Address: Hainholzweg 11, D-61462 K=C3=B6nigstein, Germany HR K=C3=B6nigstein B7522 : Ust/VAT ID DE215316329 : DUNS 34-400-1719 --20cf307810f48ca87704c87b628a Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
I'd say the simplest descriptors meeting your requirement are the p= rincipal moments of intertia, or in your case, the ratio between them.
<= br>They are trivial to compute (just Eigenvectors of the atomic coords).
On Wed, Aug 29, 2012 at 11:44 PM, Joaquin Ba= rroso Flores joaco_barroso_-_y= ahoo.com <owner-chemistry _ ccl.net> wrote:
Dear CCLers,

Is anybody awar= e if there is a molecular descriptor of the molecular length/shape and the = proper software to calculate it?
I'd like to find a way to systematically treat rod-shaped or rod-like s= haped molecules as a simple vector (with arbitrary direction imposed system= atically under a suitable criterion) in order to have a shape-size descript= or of these molecules.

Thanks in advanced for any help provided to this question.

Gree= tings from Mexico
=C2=A0
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Joaquin Barroso-F= lores, Ph. D.
Centro Conjunto de Investigacion en Quimica Sustentable Instituto de Quimica
UNAM



joaquin.barroso''a''gmail.com


"Blogastronom=C3=ADa": http://jo= aquinbarroso.blogspot.com
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D



--
Wolf-D. Ihlenfeldt -=C2=A0 Xemistry GmbH - wdi _ xemistry.com
Phone: +49 6174 201455= - Fax +49 6174 209665
---
xemistry gmbh =E2=80=93 Gesch=C3=A4ftsf=C3= =BChrer/Managing Director: Dr. W. D. Ihlenfeldt
Address: Hainholzweg 11, D-61462 K=C3=B6nigstein, Germany
HR K=C3=B6nigs= tein B7522 : Ust/VAT ID DE215316329 : DUNS 34-400-1719

--20cf307810f48ca87704c87b628a-- From owner-chemistry@ccl.net Thu Aug 30 10:17:00 2012 From: "Flick Coleman wcoleman{}wellesley.edu" To: CCL Subject: CCL: Dihedral angle: DFT vs Crystal structure Message-Id: <-47507-120830094441-30840-xT08Ewhc0dMlR6bX3QmSIw!^!server.ccl.net> X-Original-From: Flick Coleman Content-Type: multipart/alternative; boundary=0016e6de03e5109abd04c87be098 Date: Thu, 30 Aug 2012 09:43:52 -0400 MIME-Version: 1.0 Sent to CCL by: Flick Coleman [wcoleman . wellesley.edu] --0016e6de03e5109abd04c87be098 Content-Type: text/plain; charset=ISO-8859-1 I would look at the unit cell for the crystal and see how the dihedrals are situated. Often it is obvious why those particular structural features differ significantly from phase to phase (and sometimes it is not so obvious). Cheers, Flick _______________ William F. Coleman Professor of Chemistry Wellesley College Wellesley MA 02481 On Wed, Aug 29, 2012 at 2:42 AM, Adedapo Adeyinka u11335132:-:tuks.co.za < owner-chemistry*ccl.net> wrote: > Dear Gopakumar, > Like Cina said it would be impossible to > reproduce the geometry of a molecule in the solid phase with gas phase > computations. However from my experience calculations on molecules in > solvent might be able to predict the geometry in solid phase. So you can > try to do computations on your molecule using DFT with the PCM solvation > model and the UFF force field. > > Adeyinka Adedapo > Department of Chemistry, > University of Pretoria, South Africa > > On 28 August 2012 16:06, G. Gopakumar gopakumar.gopinadhan]^[gmail.com < > owner-chemistry-.-ccl.net> wrote: > >> Dear CCL members, >> >> I was calculating a molecule (71 atoms) for which the crystal >> structure is >> known. However, according to my calculation, one of the dihedral angles >> shows >> large mismatch (deviation of 12 degrees). I repeated the calculation with >> both >> B3LYP and BP86 functional and the values are given below: >> >> B3LYP/def2-TZVP ~ 21.2 >> BP86/def2-TZVP ~ 20 >> Experimental ~ 8.1 >> >> I would not worry too much if it was 2-3 degree deviation, but 12 is >> something >> that I should be careful with. >> >> I was wondering, whether there is a chance for an experimental error? Or >> is it >> just that DFT overestimates the dihedral angle? Does any body know any >> references >> where people encountered similar problem. >> >> I would be thankful for your comments >> >> with kind regards >> >> Gopakumar >> >> >> > > This message and attachments are subject to a disclaimer. Please refer to > http://www.it.up.ac.za/**documentation/governance/**disclaimer/for full details. --0016e6de03e5109abd04c87be098 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable I would look at t= he unit cell for the crystal and see how the dihedrals are situated.=A0 Oft= en it is obvious why those particular structural features differ significan= tly from phase to phase (and sometimes it is not so obvious).



Cheers,

Flick

________= _______
William= F. Coleman
Professor of Chemistry
Wellesl= ey College
Wellesley MA 02481

<= /font>




On Wed, Aug 29, 2012 at 2:42 AM, Adedapo= Adeyinka u11335132:-:tuks.co.za <= owner-chemistry*ccl.net> wrote:
Dear Gopakumar,
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0 Like Cina said it would be impossible to reproduce the geometry of a mo= lecule in the solid phase with gas phase computations. However from my expe= rience calculations on molecules in solvent might be able to predict the ge= ometry in solid phase. So you can try to do computations on your molecule u= sing DFT with=A0the PCM solvation model and the UFF force field.
=A0
Adeyinka Adedapo
Department of Chemistry,
University of Pretoria, South Africa

On 28 August 2012 16:06, G. Gopakumar gopakumar.= gopinadhan]^[gmail.com = <owner-chemistry-.-ccl.net> wrote:
Dear CCL members,

=A0=A0=A0=A0= I was calculating a molecule (71 atoms) for which the crystal structure is=
known. However, according to my calculation, one of the dihedral angles= shows
large mismatch (deviation of 12 degrees). I repeated the calculation with b= oth
B3LYP and BP86 functional and the values are given below:

B3L= YP/def2-TZVP=A0=A0 ~ 21.2
BP86/def2-TZVP=A0=A0=A0=A0 ~ 20
Experiment= al=A0=A0=A0=A0=A0=A0=A0=A0=A0 ~ 8.1

I would not worry too much if it was 2-3 degree deviation, but 12 is so= mething
that I should be careful with.

I was wondering, whether t= here is a chance for an experimental error? Or is it
just that DFT overe= stimates the dihedral angle? Does any body know any references
where people encountered similar problem.

I would be thankful for yo= ur comments

with kind regards

G= opakumar




This message and attachments are subj= ect to a disclaimer. Please refer to=20 http://www.it.u= p.ac.za/documentation/governance/disclaimer/ for full details.

--0016e6de03e5109abd04c87be098-- From owner-chemistry@ccl.net Thu Aug 30 11:30:00 2012 From: "Michel Petitjean petitjean.chiral|a|gmail.com" To: CCL Subject: CCL: rods and cylinders (was: Topological descriptor of 'molecular length') Message-Id: <-47508-120830104646-26445-C/PmJeBNd47wxWA7pcqBpg_-_server.ccl.net> X-Original-From: Michel Petitjean Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 30 Aug 2012 16:46:39 +0200 MIME-Version: 1.0 Sent to CCL by: Michel Petitjean [petitjean.chiral!=!gmail.com] Dear Joaquin, Here is my second reply to your post. Almost all molecular shape models are based on spheres, and I hope that most chemists agree that the sphere is rarely the best model for molecular shapes, even if this spherical model is useful for some applications. In fact I guess that it is often useful because it is the simplest one to use. A better one is the cylinder. Although the sphere is a one parameter shape, the cylinder is a two parameters shape: height and radius (I assumed straight cylinders). Thus there are two kinds of smallest enclosing cylinders: the smallest height enclosing cylinder and the smallest radius enclosing cylinder. Both the smallest enclosing sphere and the smallest height enclosing cylinder are easy to compute: these computations are done by the RADI freeware, already mentioned: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html However, it appears that the smallest radius enclosing cylinder is much more difficult to compute, and that is a possible explanation to the fact that minimal radii cylinders seem to be never used in molecular modeling (please tell me if you are aware of published examples of practical use of this model). But indeed it is a good model for a rod molecular shape. I myself publish a method in Appl. Alg. Eng. Comm. Comput. 2012 (DOI 10.1007/s00200-012-0171-y; preprint in arXiv 1008.5259), which has two parts: an heuristic part based on the enumeration of minimal radii circumscribed cylinders, and the minimal radii circumscribed cylinders part which itself considers the cases of circumscribed cylinders through 3, 4, and 5 points. The case of n=3 points is simple to solve. The case of n=5 points constitutes my main contribution to the field, and the solver seems to be satisfactory. Despite that the case of n=4 points offers simple equations, the solver may have difficulties to converge for some tetrahedra (most times it works, but not always). So, the full calculation may be time consuming and the returned radii is not always ensured to be the expected global minimal one. It is why I did not included this calculation in RADI. Well, an advanced version of RADI including this calculation exists, but I did not set it publicly available due to these difficulties. Nevertheless I put on my web page http://petitjeanmichel.free.fr/itoweb.petitjean.html the freeware CYL, which performs the minimal radius enclosing cylinder calculation, but not from molecular files: the input data are rather x,y,z lines (see the associated documentation). But of course, the solver is the same. Please feel free to contact me if you (or any one else) have interest in that topic. Thanks you. Best regards, Michel. 2012/8/29 Joaquin Barroso Flores joaco_barroso_-_yahoo.com : > Dear CCLers, > > Is anybody aware if there is a molecular descriptor of the molecular > length/shape and the proper software to calculate it? > I'd like to find a way to systematically treat rod-shaped or rod-like shaped > molecules as a simple vector (with arbitrary direction imposed > systematically under a suitable criterion) in order to have a shape-size > descriptor of these molecules. > > Thanks in advanced for any help provided to this question. > > Greetings from Mexico > > ======================================================= > Joaquin Barroso-Flores, Ph. D. > Centro Conjunto de Investigacion en Quimica Sustentable > Instituto de Quimica > UNAM > > -> http://joaquinbarroso.wordpress.com > > > joaquin.barroso''a''gmail.com > > > "Blogastronomía": http://joaquinbarroso.blogspot.com > ======================================================= From owner-chemistry@ccl.net Thu Aug 30 13:41:00 2012 From: "Rachelle Bienstock rachelleb1^gmail.com" To: CCL Subject: CCL: ACS CINF Symposium Announcement Message-Id: <-47509-120830133833-26825-Mzko45kY7zYPeskfe0v3vw[]server.ccl.net> X-Original-From: "Rachelle Bienstock" Date: Thu, 30 Aug 2012 13:38:32 -0400 Sent to CCL by: "Rachelle Bienstock" [rachelleb1 .. gmail.com] Announcing A Symposium organized by the ACS CINF (Division of Chemical Information): "Computational de novo ("rational") design of proteins/peptides" at the ACS Spring 2013 Meeting to be held in New Orleans, April 7-11,2013: Topics to be included: Computational de novo protein and peptide design for specific functionality; De novo enzymes from computational design; Computationally identifying mutations to confer specific functionality and properties (i.e. additional stability or interaction specificity); Directed enzyme evolution; Designing proteins from simple motifs; Applications of database-driven tools in computational protein design. ABSTRACT SUBMISSION DEADLINE: OCTOBER 15, 2012 Please submit abstracts through the ACS (American Chemical Society) online system https://portal.acs.org/portal/acs/corg/memberapp?_nfpb=true&_pageLabel=mapp_marathon_login_page&toURL=http%3A%2F%2Fabstracts.acs.org%2Findex2.php?frm=1 See (http://portal.acs.org/portal/acs/corg/content?_nfpb=true&_pageLabel=PP_SUPERARTICLE&node_id=879&use_sec=false&sec_url_var=region1&__uuid=ede7763f-5cb3-484e-bba1-79ecac8a1545) for additional information regarding the meeting. From owner-chemistry@ccl.net Thu Aug 30 14:38:00 2012 From: "David A Mannock dmannock(!)ualberta.ca" To: CCL Subject: CCL: Topological descriptor of 'molecular length' Message-Id: <-47510-120830140938-1377-brFwDM2sEJoBrV+3VzjTiA---server.ccl.net> X-Original-From: David A Mannock Content-Type: multipart/alternative; boundary=f46d04088c7fa1af2304c87f9351 Date: Thu, 30 Aug 2012 12:09:30 -0600 MIME-Version: 1.0 Sent to CCL by: David A Mannock [dmannock[a]ualberta.ca] --f46d04088c7fa1af2304c87f9351 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Joaquin, There is a simple online java script called "moldiam". It uses pdb files. Remember to minimize your sructures first. I also overlay multiple analogues in another application before making comparisons to correct for axis issues. Differences with the literature values may also arise because of different alignment points. For example some sterols are aligned relative to the C3-C17 axis of the ring structure. The app is quick as easy to use for a first estimate, but beware its limitations. I agree with the other posts in this thread about the use of other shape and moment decriptors. However, be sure that you pick the right moment as a descriptor for your system. Dave http://moldiam.bio-log-software.com/ On Wed, Aug 29, 2012 at 3:44 PM, Joaquin Barroso Flores joaco_barroso_-_yahoo.com wrote: > Dear CCLers, > > Is anybody aware if there is a molecular descriptor of the molecular > length/shape and the proper software to calculate it? > I'd like to find a way to systematically treat rod-shaped or rod-like > shaped molecules as a simple vector (with arbitrary direction imposed > systematically under a suitable criterion) in order to have a shape-size > descriptor of these molecules. > > Thanks in advanced for any help provided to this question. > > Greetings from Mexico > > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D > Joaquin Barroso-Flores, Ph. D. > Centro Conjunto de Investigacion en Quimica Sustentable > Instituto de Quimica > UNAM > > -> http://joaquinbarroso.wordpress.com > > > joaquin.barroso''a''gmail.com > > > "Blogastronom=EDa": http://joaquinbarroso.blogspot.com > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D > --f46d04088c7fa1af2304c87f9351 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Joaquin, There is a simple online java script called "moldiam". I= t uses pdb files. Remember to minimize your sructures first. I also overlay= multiple analogues in another application before making comparisons to cor= rect for axis issues. Differences with the literature values may also arise= because of different alignment points. For example some sterols are aligne= d relative to the C3-C17 axis of the ring structure. The app is quick as ea= sy to use for a first estimate, but beware its limitations. I agree with th= e other posts in this thread about the use of other shape and moment decrip= tors. However, be sure that you pick the right moment as a descriptor for y= our system. Dave

http://moldiam.bio-log= -software.com/


On Wed, Aug 29, 20= 12 at 3:44 PM, Joaquin Barroso Flores joaco_barroso_-_yahoo.com <owner-chemistry===ccl.net&g= t; wrote:
Dear CCLers,

Is anybody awar= e if there is a molecular descriptor of the molecular length/shape and the = proper software to calculate it?
I'd like to find a way to systematically treat rod-shaped or rod-like s= haped molecules as a simple vector (with arbitrary direction imposed system= atically under a suitable criterion) in order to have a shape-size descript= or of these molecules.

Thanks in advanced for any help provided to this question.

Gree= tings from Mexico
=A0
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Joaquin Barroso-Flor= es, Ph. D.
Centro Conjunto de Investigacion en Quimica Sustentable
Instituto de Quimica
UNAM



joaquin.barroso''a''gmail.com


"Blogastronom=EDa": http://jo= aquinbarroso.blogspot.com
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D

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