From owner-chemistry@ccl.net Tue Aug 21 03:14:01 2007
From: "soumya samineni soumya_samineni^-^rediffmail.com" <owner-chemistry_+_server.ccl.net>
To: CCL
Subject: CCL: surface construction
Message-Id: <-34960-070821030944-32440-bCIx+G3ltLy1bhp6NBoEIA_+_server.ccl.net>
X-Original-From: "soumya samineni" <soumya_samineni[#]rediffmail.com>
Date: Tue, 21 Aug 2007 03:09:37 -0400
Sent to CCL by: "soumya samineni" [soumya_samineni : rediffmail.com]
I have made a 111 surface of FCC metal with 3X3 atoms.
now i would like to adsorb Si over it with different coverages.
how can i do that ..? (single Si prefres HCP site)
Can some one send me the coordinates for different coverages that you would have generated for ur studies.
thanx in advace
soumya
From owner-chemistry@ccl.net Tue Aug 21 04:57:01 2007
From: "Egon Willighagen egon.willighagen**gmail.com" <owner-chemistry+*+server.ccl.net>
To: CCL
Subject: CCL: Open Source 3D coordinate generation tool
Message-Id: <-34961-070821044951-17511-NOMRagMlHv97xt5EuExcvQ+*+server.ccl.net>
X-Original-From: "Egon Willighagen" <egon.willighagen%x%gmail.com>
Content-Disposition: inline
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Date: Tue, 21 Aug 2007 08:54:19 +0200
MIME-Version: 1.0
Sent to CCL by: "Egon Willighagen" [egon.willighagen~~gmail.com]
Dear Rajarshi,
On 8/20/07, Rajarshi Guha rguha^^indiana.edu <owner-chemistry.:.ccl.net> wrote:
> Sent to CCL by: Rajarshi Guha [rguha===indiana.edu]
> The program and instructions of compiling and usage can be obtained
> from http://www.chembiogrid.org/cheminfo/smi23d/
is the service also available via SOAP?
Egon
--
----
http://chem-bla-ics.blogspot.com/
From owner-chemistry@ccl.net Tue Aug 21 08:59:00 2007
From: "Jon Lyon jtl3z]~[virginia.edu" <owner-chemistry---server.ccl.net>
To: CCL
Subject: CCL: conversion to xyz
Message-Id: <-34962-070821075507-15804-2MQoujLY+47KVWgYVJ67Yg---server.ccl.net>
X-Original-From: "Jon Lyon" <jtl3z^-^virginia.edu>
Date: Tue, 21 Aug 2007 07:55:02 -0400
Sent to CCL by: "Jon Lyon" [jtl3z*_*virginia.edu]
Does anyone know of a program (or have a script) to convert the atomic distances of a molecule to an xyz file (or z-matrix)?
Thanks if advance
From owner-chemistry@ccl.net Tue Aug 21 09:33:00 2007
From: "Richard Leo Wood woodx278[-]umn.edu" <owner-chemistry%x%server.ccl.net>
To: CCL
Subject: CCL: Fractional coordinates to cartesian
Message-Id: <-34963-070821091333-12765-116502yWuftdgcGlQPaK1A%x%server.ccl.net>
X-Original-From: "Richard Leo Wood" <woodx278_-_umn.edu>
Date: Tue, 21 Aug 2007 09:13:29 -0400
Sent to CCL by: "Richard Leo Wood" [woodx278 ~~ umn.edu]
Hi all,
Do any of you know of any program (free?) that will convert fractional coordinates to cartesian coordinates? If not in a program, is there a method that can be used to do it? I spent most of yesterday searching for something, but I came up empty.
I have a few crystal structures in fractional coordinates (in papers, so I don't have them in electronic format) that I need converted to cartesian to compare them to some calculations that I have done.
TIA,
Richard
Richard L. Wood, Ph. D.
University of Minnesota
Dept. of Medicinal Chemistry,
College of Pharmacy
717 Delaware St. SE
Minneapolis, MN 55414-2959
woodx278|*|umn.edu
From owner-chemistry@ccl.net Tue Aug 21 11:28:00 2007
From: "Saman Alavi saman.alavi-,-nrc.ca" <owner-chemistry ~ server.ccl.net>
To: CCL
Subject: CCL: Fractional coordinates to cartesian
Message-Id: <-34964-070821112249-24771-D7zuo+GS+2jQeIZKLozYSQ ~ server.ccl.net>
X-Original-From: Saman Alavi <saman.alavi\a/nrc.ca>
Content-Type: multipart/alternative;
boundary="------------090904090701090107080502"
Date: Tue, 21 Aug 2007 10:50:42 -0400
MIME-Version: 1.0
Sent to CCL by: Saman Alavi [saman.alavi() nrc.ca]
This is a multi-part message in MIME format.
--------------090904090701090107080502
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Hi Richard,
Can you find the fractional coordinates in the cif formate? If so, you
can use Mercury to read the file and output the data as cartesian
coordinates.
If not, the conversion is rather straightforward to do by hand. I can
send you a short Word Document on how the conversion is done with
knowledge of the unit cell vectors. Basically, the fractional
coordinates show the fraction of each unit cell vector that contributes
to the position of that atom.
x_cart = *A*_x * frac_a + *B*_x * frac_b + *C_x* * frac_c
y_cart = *A*_y * frac_a + *B*_y * frac_b + *C_y* * frac_c
z_cart = *A*_z * frac_a + *B*_z * frac_b + *C_z* * frac_c
where *A*, *B*, and *C* are the unit cell vectors and *A*_x is the
x-coordinate of unit cell vector *A*.
best regards,
Saman
Richard Leo Wood woodx278[-]umn.edu wrote:
> Sent to CCL by: "Richard Leo Wood" [woodx278 ~~ umn.edu]
> Hi all,
>
> Do any of you know of any program (free?) that will convert fractional coordinates to cartesian coordinates? If not in a program, is there a method that can be used to do it? I spent most of yesterday searching for something, but I came up empty.
>
> I have a few crystal structures in fractional coordinates (in papers, so I don't have them in electronic format) that I need converted to cartesian to compare them to some calculations that I have done.
>
> TIA,
> Richard
>
>
> Richard L. Wood, Ph. D.
> University of Minnesota
> Dept. of Medicinal Chemistry,
> College of Pharmacy
> 717 Delaware St. SE
> Minneapolis, MN 55414-2959
> woodx278[]umn.edu>
>
>
>
>
--------------090904090701090107080502
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Hi Richard,<br>
<br>
Can you find the fractional coordinates in the cif formate? If so, you
can use Mercury to read the file and output the data as cartesian
coordinates.<br>
<br>
If not, the conversion is rather straightforward to do by hand. I can
send you a short Word Document on how the conversion is done with
knowledge of the unit cell vectors. Basically, the fractional
coordinates show the fraction of each unit cell vector that contributes
to the position of that atom.<br>
<br>
x_cart = <b>A</b>_x * frac_a + <b>B</b>_x * frac_b + <b>C_x</b>
* frac_c<br>
y_cart = <b>A</b>_y * frac_a + <b>B</b>_y * frac_b + <b>C_y</b>
* frac_c<br>
z_cart = <b>A</b>_z * frac_a + <b>B</b>_z * frac_b + <b>C_z</b>
* frac_c<br>
<br>
where <b>A</b>, <b>B</b>, and <b>C</b> are the unit cell vectors and
<b>A</b>_x is the x-coordinate of unit cell vector <b>A</b>.<br>
<br>
best regards,<br>
Saman<br>
<br>
Richard Leo Wood woodx278[-]umn.edu wrote:
<blockquote
cite="mid:-id%233q2-34963-070821091333-12765-f4LV2Dbs3gGyu38QZflnmg*_*server.ccl.net"
type="cite">
<pre wrap="">Sent to CCL by: "Richard Leo Wood" [woodx278 ~~ umn.edu]
Hi all,
Do any of you know of any program (free?) that will convert fractional coordinates to cartesian coordinates? If not in a program, is there a method that can be used to do it? I spent most of yesterday searching for something, but I came up empty.
I have a few crystal structures in fractional coordinates (in papers, so I don't have them in electronic format) that I need converted to cartesian to compare them to some calculations that I have done.
TIA,
Richard
Richard L. Wood, Ph. D.
University of Minnesota
Dept. of Medicinal Chemistry,
College of Pharmacy
717 Delaware St. SE
Minneapolis, MN 55414-2959
woodx278[]umn.eduE-mail to subscribers: <a class="moz-txt-link-abbreviated" href="mailto:CHEMISTRY*_*ccl.net">CHEMISTRY*_*ccl.net</a> or use:
<a class="moz-txt-link-freetext" href="http://www.ccl.net/cgi-bin/ccl/send_ccl_message">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a>
E-mail to administrators: <a class="moz-txt-link-abbreviated" href="mailto:CHEMISTRY-REQUEST*_*ccl.net">CHEMISTRY-REQUEST*_*ccl.net</a> or use
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Before posting, check wait time at: <a class="moz-txt-link-freetext" href="http://www.ccl.net">http://www.ccl.net</a>
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RTFI: <a class="moz-txt-link-freetext" href="http://www.ccl.net/chemistry/aboutccl/instructions/">http://www.ccl.net/chemistry/aboutccl/instructions/</a</pre>
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--------------090904090701090107080502--
From owner-chemistry@ccl.net Tue Aug 21 12:17:01 2007
From: "Geoffrey Hutchison geoffh(!)pitt.edu" <owner-chemistry-#-server.ccl.net>
To: CCL
Subject: CCL: Fractional coordinates to cartesian
Message-Id: <-34965-070821114158-1264-SmRlYB83LpOK2h4hnl+Uww-#-server.ccl.net>
X-Original-From: Geoffrey Hutchison <geoffh|pitt.edu>
Content-Transfer-Encoding: 7bit
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Date: Tue, 21 Aug 2007 10:30:03 -0400
Mime-Version: 1.0 (Apple Message framework v752.2)
Sent to CCL by: Geoffrey Hutchison [geoffh!=!pitt.edu]
> I have a few crystal structures in fractional coordinates (in
> papers, so I don't have them in electronic format) that I need
> converted to cartesian to compare them to some calculations that I
> have done.
Open Babel supports a "free-form fractional" file format for exactly
this purpose. You can convert them to whatever output format with
babel. (I had exactly the same problem, which is why it's supported.)
http://openbabel.sourceforge.net/wiki/Free_Form_Fractional
Cheers,
-Geoff
-------------------------------------------
Geoff Hutchison
Assistant Professor
University of Pittsburgh, Department of Chemistry
219 Parkman Avenue
Pittsburgh, PA 15260
From owner-chemistry@ccl.net Tue Aug 21 12:58:02 2007
From: "Close, David M. CLOSED()mail.etsu.edu" <owner-chemistry:+:server.ccl.net>
To: CCL
Subject: CCL: Fractional coordinates to cartesian
Message-Id: <-34966-070821114457-3037-ZBNo5/PuRXyy5Hfd3L33lw:+:server.ccl.net>
X-Original-From: "Close, David M." <CLOSED(a)mail.etsu.edu>
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Date: Tue, 21 Aug 2007 10:22:21 -0400
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Sent to CCL by: "Close, David M." [CLOSED=mail.etsu.edu]
Richard:
This is very easy to do in BABEL. You can find BABEL on in www, and
it is easy to set up in Windows or UNIX.
Then just use a one line command:
Babel -if sourcename -ox outputname
Where -i means input, f means fractional
and -o means output and x means xyz.
In your second paragraph you mention a common problem with old crystal
papers. It is a real pain to have to type in the xyz coordinates. But
these can be found in sites like the Cambridge or the PDB at Rutgers.
Regards, Dave Close.
-----Original Message-----
> From: owner-chemistry*ccl.net [mailto:owner-chemistry*ccl.net]
Sent: Tuesday, August 21, 2007 9:13 AM
To: Close, David M.
Subject: CCL: Fractional coordinates to cartesian
Sent to CCL by: "Richard Leo Wood" [woodx278 ~~ umn.edu]
Hi all,
Do any of you know of any program (free?) that will convert fractional
coordinates to cartesian coordinates? If not in a program, is there a
method that can be used to do it? I spent most of yesterday searching
for something, but I came up empty.
I have a few crystal structures in fractional coordinates (in papers, so
I don't have them in electronic format) that I need converted to
cartesian to compare them to some calculations that I have done.
TIA,
Richard
Richard L. Wood, Ph. D.
University of Minnesota
Dept. of Medicinal Chemistry,
College of Pharmacy
717 Delaware St. SE
Minneapolis, MN 55414-2959
woodx278[]umn.eduhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt
From owner-chemistry@ccl.net Tue Aug 21 13:43:01 2007
From: "Igor Filippov Contr igorf(!)helix.nih.gov" <owner-chemistry]|[server.ccl.net>
To: CCL
Subject: CCL: Open Source 3D coordinate generation tool
Message-Id: <-34967-070821124452-9398-6FSp5qT5fshJ0OD9khptIQ]|[server.ccl.net>
X-Original-From: "Igor Filippov [Contr]" <igorf(-)helix.nih.gov>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain
Date: Tue, 21 Aug 2007 12:44:25 -0400
Mime-Version: 1.0
Sent to CCL by: "Igor Filippov [Contr]" [igorf .. helix.nih.gov]
Rajarshi,
This is a great development, and I'm sure it will be welcomed by many!
Congratulations!
A couple questions:
- Is there any specific reason for Apache license? Do you think it might
present difficulties for people who'd like to include this project in
their GPL code?
- smi2sdf program seems to include an empty "name" property in the sd
output, and mengine has an empty "title" property - it might confuse
some other programs.
- mengine seems to miss empty lines between the properties it adds, for
example:
> <MMFF94 energy>
103.559373
> <dipole moment>
2.838407
> <xLogP>
2.325000
> <Point Group>
Cs
> <Moments of Inertia>
176.5185858.3 251.5937198.3 356.2962958.3
> <thermodynamics dE, dH, S, dG, CP>
321.6609508.3 322.2533578.3 108.7103818.3 289.8413708.3 71.9372568.3
I could be wrong, but it might also cause problems with some third party
tools...
Best regards and keep up the good work :)
Igor
On Mon, 2007-08-20 at 15:12 -0400, Rajarshi Guha rguha^^indiana.edu
wrote:
> Sent to CCL by: Rajarshi Guha [rguha===indiana.edu]
> Hi,
> we have released a 3D coordinate generation tool called smi23d
> which will convert a SMILES string to a 3D structure. The program
> consists of two separate components: smi2sdf which converts a SMILES
> string to a 'rough' set of 3D coordinates using the stochastic
> proximity embedding (SPE) algorithm. Given the initial rough
> coordinates, the program called mengine then optimizes them using the
> MMFF94 forcefield to give a reasonable low energy structure.
>
> Note: these programs will only generate a single 3D structure.
>
> The code is written in C and is currently in the form of two
> standalone programs. In the future we plan to convert it to a library
> to ease inclusion within other systems. The software is released
> under the Apache 2.0 license.
>
> The program and instructions of compiling and usage can be obtained
> > from http://www.chembiogrid.org/cheminfo/smi23d/
>
> At this point we have not performed significant benchmarking, mainly
> due to lack of access to other programs. However we welcome any
> comparisons with other programs and would be happy to help out in
> such efforts.
>
> We have used smi3d to convert about 99% of PubChem to 3D, the results
> of which are stored in a database which can be accessed at http://
> www.chembiogrid.org/cheminfo/p3d/.
>
> -------------------------------------------------------------------
> Rajarshi Guha <rguha###indiana.edu>
> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE
> -------------------------------------------------------------------
> Despite the high cost of living, it remains popular.
From owner-chemistry@ccl.net Tue Aug 21 14:03:01 2007
From: "Shrinwantu Pal paul++jncasr.ac.in" <owner-chemistry{=}server.ccl.net>
To: CCL
Subject: CCL:G: solvent scipcm
Message-Id: <-34968-070821054349-8480-dkjwq3nhUP+ilLT9vJfziA{=}server.ccl.net>
X-Original-From: "Shrinwantu Pal" <paul|-|jncasr.ac.in>
Content-Transfer-Encoding: 8bit
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Date: Tue, 21 Aug 2007 15:18:55 +0530 (IST)
MIME-Version: 1.0
Sent to CCL by: "Shrinwantu Pal" [paul ~~ jncasr.ac.in]
Dear CCLers,
i am running a solvent calculation in Gaussian 03 with SCRF SCIPCM model
and THF as the solvent.
But the job gets killed saying:
"WARNING! Serious error in surface integrals.
Nuclear flux = 98.27 Qnuc = 100.00 Error in int = 0.00
It is probable that some of the solute is outside the cavity and/or
parts of the cavity surface cannot be reached from the origin.
Try more integration points or a different set of integration origins.
Surface Problems in SciFoc"
i have no clue..
how can i increase the integration points?
how much does the cavity include?
i will really be indebted for any advice.
Shrinwantu Pal
TSU
JNCASR India
From owner-chemistry@ccl.net Tue Aug 21 14:41:01 2007
From: "Rajarshi Guha rguha!^!indiana.edu" <owner-chemistry]![server.ccl.net>
To: CCL
Subject: CCL: Open Source 3D coordinate generation tool
Message-Id: <-34969-070821091741-14746-Yn2ul88nuJd1q4m2zSe40g]![server.ccl.net>
X-Original-From: Rajarshi Guha <rguha[A]indiana.edu>
Content-Transfer-Encoding: 7bit
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Date: Tue, 21 Aug 2007 07:38:30 -0400
Mime-Version: 1.0 (Apple Message framework v752.3)
Sent to CCL by: Rajarshi Guha [rguha^-^indiana.edu]
On Aug 21, 2007, at 2:54 AM, Egon Willighagen
egon.willighagen**gmail.com wrote:
>
> Sent to CCL by: "Egon Willighagen" [egon.willighagen~~gmail.com]
> Dear Rajarshi,
>
> On 8/20/07, Rajarshi Guha rguha^^indiana.edu <owner-chemistry-,-
> ccl.net> wrote:
>> Sent to CCL by: Rajarshi Guha [rguha===indiana.edu]
>> The program and instructions of compiling and usage can be obtained
>> from http://www.chembiogrid.org/cheminfo/smi23d/
>
> is the service also available via SOAP?
No, we haven't put the 3D structure generator up as a service yet.
-------------------------------------------------------------------
Rajarshi Guha <rguha]*[indiana.edu>
GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE
-------------------------------------------------------------------
Entropy isn't what it used to be.
From owner-chemistry@ccl.net Tue Aug 21 17:25:01 2007
From: "Michel Petitjean ptitjean#itodys.jussieu.fr" <owner-chemistry:+:server.ccl.net>
To: CCL
Subject: CCL: conversion to xyz
Message-Id: <-34970-070821172119-26970-5cY3l86rit5A2Rgsg74OWQ:+:server.ccl.net>
X-Original-From: Michel Petitjean <ptitjean^^^itodys.jussieu.fr>
Date: Tue, 21 Aug 2007 23:21:06 +0200 (MEST)
Sent to CCL by: Michel Petitjean [ptitjean(-)itodys.jussieu.fr]
To: chemistry],[ccl.net
Subject: CCL: Re: conversion to xyz
Look at "multidimensional scaling" with google: it is the algorithm
converting a n*n distance matrix (well, the matrix is symmetric and
its diagonal elements are null) into a n*d matrix of cartesian
coordinates, assuming that the distances are measured in the
d-dimensional euclidean space.
Here you have to set d=3.
For those who are interested to use the method with distances
issued from a connex molecular graph, note that the multidimensional
scaling needs euclidean distances. Adding a constant to the
distances (as recommended in some books when the distance
is not euclidean) permits to run the algorithm, but the
coordinates generated for molecular graphs after projection
in a 3D space give a rather poor result.
Michel Petitjean, Email: petitjean],[itodys.jussieu.fr
ITODYS (CNRS, UMR 7086)
1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57
75005 Paris, France. FAX : +33 (0)1 44 27 68 14
http://petitjeanmichel.free.fr/itoweb.petitjean.shape.html
Sent to CCL by: "Jon Lyon" [jtl3z*_*virginia.edu]
> Does anyone know of a program (or have a script) to convert the atomic distances of a molecule to an xyz file (or z-matrix)?
>
> Thanks if advance
From owner-chemistry@ccl.net Tue Aug 21 18:11:01 2007
From: "LI Daobing lidaobing+ccl|-|gmail.com" <owner-chemistry.:.server.ccl.net>
To: CCL
Subject: CCL: conversion to xyz
Message-Id: <-34971-070821180911-17783-wFg8JQggROeJHogp6+mtQA.:.server.ccl.net>
X-Original-From: "LI Daobing" <lidaobing+ccl[-]gmail.com>
Content-Disposition: inline
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=ISO-8859-1
Date: Wed, 22 Aug 2007 06:08:49 +0800
MIME-Version: 1.0
Sent to CCL by: "LI Daobing" [lidaobing+ccl()gmail.com]
On 8/22/07, Michel Petitjean ptitjean#itodys.jussieu.fr
<owner-chemistry^ccl.net> wrote:
>
> Sent to CCL by: Michel Petitjean [ptitjean(-)itodys.jussieu.fr]
> To: chemistry_+_ccl.net
> Subject: CCL: Re: conversion to xyz
>
> Look at "multidimensional scaling" with google: it is the algorithm
> converting a n*n distance matrix (well, the matrix is symmetric and
> its diagonal elements are null) into a n*d matrix of cartesian
> coordinates, assuming that the distances are measured in the
> d-dimensional euclidean space.
> Here you have to set d=3.
> For those who are interested to use the method with distances
> issued from a connex molecular graph, note that the multidimensional
> scaling needs euclidean distances. Adding a constant to the
> distances (as recommended in some books when the distance
> is not euclidean) permits to run the algorithm, but the
> coordinates generated for molecular graphs after projection
> in a 3D space give a rather poor result.
>
> Michel Petitjean, Email: petitjean_+_itodys.jussieu.fr
> ITODYS (CNRS, UMR 7086)
> 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57
> 75005 Paris, France. FAX : +33 (0)1 44 27 68 14
> http://petitjeanmichel.free.fr/itoweb.petitjean.shape.html
>
> Sent to CCL by: "Jon Lyon" [jtl3z*_*virginia.edu]
> > Does anyone know of a program (or have a script) to convert the atomic distances of a molecule to an xyz file (or z-matrix)?
> >
In a common case(for example, data from NMR), the full matrix of
distance is not available. under this case, you should consider
distance geometry, there is a small review in the book of A.R.
Leach(Molecular Modelling, Principles and Applications, 2nd Ed., A. R.
Leach, 2001, Section 9.5)
I also remember concoord[1] can deal with this problem, but I am not sure.
[1] http://www.mpibpc.gwdg.de/groups/de_groot/concoord/
--
LI Daobing
From owner-chemistry@ccl.net Tue Aug 21 21:13:00 2007
From: "Siegfried Hoefinger shoefing(0)mtu.edu" <owner-chemistry|-|server.ccl.net>
To: CCL
Subject: CCL:G: polch_2.1
Message-Id: <-34972-070821145525-16869-pT6mV+gSJBoRYgYIYPaYxA|-|server.ccl.net>
X-Original-From: "Siegfried Hoefinger" <shoefing**mtu.edu>
Date: Tue, 21 Aug 2007 14:55:22 -0400
Sent to CCL by: "Siegfried Hoefinger" [shoefing##mtu.edu]
Dear all,
POLCH 2.1 has become available via
--> http://mammoth3.gup.uni-linz.ac.at/~polch
POLCH is an implicit solvation program for proteins
( residues < 500). It is based on the Poisson-Boltzmann
approach and has the following characteristics,
a) all expensive parts of the calculation are carried out
on the specialized computer chip MD-GRAPE-2
b) consideration of electrostatic as well as non-polar
contributions
c) PCM-like decomposition into properly separated individual
contributions
d) usage of Gaussian cube format for ESP maps (electrostatic
potentials) for straightforward visualization with VMD
or MOLDEN
e) support of several solvents, ie water, ethanol, n-octanol
It is still all very much in a premature stage and therefore
any comments/suggestions/experiences are greatly appreciated.
best
sig
--
Siegfried Hoefinger, PhD
Michigan Technological University
Department of Physics
836 Dow Building
1400 Townsend Drive
Houghton, Michigan, 49931 - 1295, USA
From owner-chemistry@ccl.net Tue Aug 21 21:48:00 2007
From: "Rajarshi Guha rguha:-:indiana.edu" <owner-chemistry[-]server.ccl.net>
To: CCL
Subject: CCL: Open Source 3D coordinate generation tool
Message-Id: <-34973-070821154936-14205-AA+PzJeLLvMgYVhXJU78SQ[-]server.ccl.net>
X-Original-From: Rajarshi Guha <rguha{:}indiana.edu>
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Date: Tue, 21 Aug 2007 15:22:04 -0400
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Sent to CCL by: Rajarshi Guha [rguha]_[indiana.edu]
On Aug 21, 2007, at 12:44 PM, Igor Filippov Contr igorf(!)
helix.nih.gov wrote:
>
> Sent to CCL by: "Igor Filippov [Contr]" [igorf .. helix.nih.gov]
> Rajarshi,
>
> This is a great development, and I'm sure it will be welcomed by many!
> Congratulations!
Thank you!
> - Is there any specific reason for Apache license? Do you think it
> might
> present difficulties for people who'd like to include this project in
> their GPL code?
My understanding is that the Apache license is very permissive and
that the code can be included in GPL and related code.
> - smi2sdf program seems to include an empty "name" property in the sd
> output, and mengine has an empty "title" property - it might confuse
> some other programs.
Did the input SMILES have a title - I think that maybe the reason
> - mengine seems to miss empty lines between the properties it adds,
> for
> example:
We'll take a look at these problems and see what's going on
-------------------------------------------------------------------
Rajarshi Guha <rguha^indiana.edu>
GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE
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After a number of decimal places, nobody gives a damn.