From owner-chemistry@ccl.net Wed Nov 9 08:27:00 2005
From: "Kim Branson kim.branson\a/gmail.com" <owner-chemistry..server.ccl.net>
To: CCL
Subject: CCL: Active site volume and surface exposure
Message-Id: <-29908-051109012456-23627-wBzRzJXyANFlptQ3dmwg1g..server.ccl.net>
X-Original-From: Kim Branson <kim.branson!A!gmail.com>
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Date: Wed, 9 Nov 2005 16:27:51 +1100
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Sent to CCL by: Kim Branson [kim.branson(~)gmail.com]
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Hi all,
I'm currently looking for a method that can determine the volume of an
active site and its surface exposure. I'm conducting a validation study
on protein-protein interaction inhibitors and i would like to quantify
the oft heard expression "protein-protein interfaces are often flat
featureless surfaces". I'd like to compare the binding sites to that of
other systems, and hopefully examine the relationship between scoring
function performance and active site volume/surface exposure.
I have a crude metric using the ratio of the volume of the active site
to the total solvent accessible surface of my defined binding region. I
feel there might be a better way to do this.
cheers
Kim
Dr Kim Branson
Peter Doherty Fellow
Protein Structure and Function
St Vincents Institute for Medical Research
41 Victoria Parade, Fitzroy
Victoria 3065, Australia.
Phone: +613 9288 2480
Fax: +613 94162 676
Ph +613 9662 7136
kbranson(0)svi.edu.au
kim.branson(0)gmail.com
www.svi.edu.au
"Reminds me of the time I went to Africa, someone forgot the corkscrew
and we had to live on food and water for days."
W.C. Fields
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From owner-chemistry@ccl.net Wed Nov 9 09:48:00 2005
From: "Telkuni Tsuru telkuni .. venus.dti.ne.jp" <owner-chemistry/./server.ccl.net>
To: CCL
Subject: CCL:G: Multi-step ONIOM
Message-Id: <-29909-051109092652-11785-KPPi6HPLg9IjMnTD0WXSQQ/./server.ccl.net>
X-Original-From: "Telkuni Tsuru" <telkuni~~venus.dti.ne.jp>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain;
charset="iso-2022-jp"
Date: Wed, 9 Nov 2005 23:26:51 +0900
MIME-Version: 1.0
Sent to CCL by: "Telkuni Tsuru" [telkuni]-[venus.dti.ne.jp]
Hello, CCLers.
I like to ask the description of multi-step ONIOM job on Gaussian98W.
For example, the following input is correct?
======= input ========
%Chk=NaCl
#T ONIOM(HF/6-31G(d):HF/3-21G(d)) SP
NaCl SinglePoint-1 Na(High) Cl(Low)
0,1 0,1
Na 2.000000 0.000000 0.000000 H
Cl 0.000000 0.000000 0.000000 L
--Link1--
%Chk=NaCl
#T ONIOM(HF/6-311+G(d,p):HF/6-31G(d)) SP Geom=Check Guess=Read
NaCl SinglePoint-2 Na(High) Cl(Low)
0,1 0,1
Na H
Cl L
======= end of input =======
If you don't mind, please point out the wrong part and teach me correct
description.
Any responses I'll appreciate. I will summarize them and upload to this ML.
Sincerely yours,
----------------------------------------------------
Telkuni Tsuru telkuni[-]venus.dti.ne.jp
Bunshi Gijyutu
[this "venus" means the planet "venus".]
From owner-chemistry@ccl.net Wed Nov 9 11:04:01 2005
From: "errol lewars elewars-x-trentu.ca" <owner-chemistry{}server.ccl.net>
To: CCL
Subject: CCL:G: transition state searches with CASSCF ???
Message-Id: <-29910-051109102832-10194-Wk+b5qgVNseNQqT8BPfVZQ{}server.ccl.net>
X-Original-From: errol lewars <elewars(a)trentu.ca>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=us-ascii; format=flowed
Date: Wed, 09 Nov 2005 10:26:17 -0500
MIME-Version: 1.0
Sent to CCL by: errol lewars [elewars-,-trentu.ca]
2005 Nov 9
Hello,
Yes, it is possible to find a TS at the CASSCF level with G03 (I used
revision B.05); see J Phys Chem 2005, 109(43), 9827-9830. Start with a
HF or MP2 structure, say, for the input geometry. Use corresponding MOs
for the active space in comparing reactant, TS, and product.
However your reaction, in which closed-shell molecules are transformed
into radicals may give special problems in calculating the activation
energy.
EL
====
Theo de Bruin theodorus.de-bruin!^!ifp.fr wrote:
>Sent to CCL by: "Theo de Bruin" [theodorus.de-bruin%a%ifp.fr]
>Hello
>
>I wish to know whether it is possible to perform transition state searches at the CASSCF level of theory using Gaussian 03 rev C02. I asked the same question to the helpdesk of Gaussian but I gave up, after waiting more than 5 weeks.
>I would like to study a bi-molecular reaction in which two (neutral) molecules are transformed into two radicals (reversed dismutation reaction).
>Neither B3LYP nor X3LYP are capable to locate the TS, while unrestricted MP2 gives the correct TS but unusual high barrier (delta H activation) and delta H are obtained.
>
>Thanks for sharing your thoughts how to handle this problem.
>
>Kind regards,
>
>Theo de Bruin
>theodorus.de-bruin . ifp.fr>
>
>
>
>
From owner-chemistry@ccl.net Wed Nov 9 12:37:00 2005
From: "Elaine Meng meng|,|cgl.ucsf.edu" <owner-chemistry(!)server.ccl.net>
To: CCL
Subject: CCL: Active site volume and surface exposure
Message-Id: <-29911-051109123443-28595-1lXP93zWATjWcqWbiIZ5WA(!)server.ccl.net>
X-Original-From: Elaine Meng <meng!^!cgl.ucsf.edu>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
Date: Wed, 9 Nov 2005 08:57:12 -0800
Mime-Version: 1.0 (Apple Message framework v746.2)
Sent to CCL by: Elaine Meng [meng ~ cgl.ucsf.edu]
Hi Kim,
The following papers used an RMS distance of interface atoms to
a least-squares plane (there are many more papers, but these will
get you started):
Jones and Thornton.
Prediction of protein-protein interaction sites using patch analysis.
J Mol Biol. 1997 Sep 12;272(1):133-43.
Chakrabarti and Janin.
Dissecting protein-protein recognition sites.
Proteins. 2002 May 15;47(3):334-43.
Another measure I've seen is length to width to depth:
Preissner, Goede, and Frommel.
Dictionary of interfaces in proteins (DIP).
Data bank of complementary molecular surface patches.
J Mol Biol. 1998 Jul 17;280(3):535-50.
Hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D. meng{=}cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
http://www.cgl.ucsf.edu/home/meng/index.html
> Sent to CCL by: Kim Branson [kim.branson(~)gmail.com]
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
>
> Hi all,
>
> I'm currently looking for a method that can determine the volume of an
> active site and its surface exposure. I'm conducting a validation
> study
> on protein-protein interaction inhibitors and i would like to quantify
> the oft heard expression "protein-protein interfaces are often flat
> featureless surfaces". I'd like to compare the binding sites to
> that of
> other systems, and hopefully examine the relationship between scoring
> function performance and active site volume/surface exposure.
>
> I have a crude metric using the ratio of the volume of the active site
> to the total solvent accessible surface of my defined binding
> region. I
> feel there might be a better way to do this.
>
> cheers
>
> Kim
From owner-chemistry@ccl.net Wed Nov 9 13:11:00 2005
From: "Ferenc Csizmadia fcsiz^^^chemaxon.com" <owner-chemistry * server.ccl.net>
To: CCL
Subject: CCL: InChI in Marvin, JChem, ....
Message-Id: <-29912-051109125846-17775-symDzLKxK28Vc1o5rFyrgA * server.ccl.net>
X-Original-From: Ferenc Csizmadia <fcsiz*o*chemaxon.com>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=ISO-8859-2; format=flowed
Date: Wed, 09 Nov 2005 18:58:27 +0100
MIME-Version: 1.0
Sent to CCL by: Ferenc Csizmadia [fcsiz^chemaxon.com]
Hi,
(Sorry for cross-posting)
InChI import and export have been added into ChemAxon tools
(www.chemaxon.com/products.html)
At the moment Linux, Windows and Mac platforms are supported, but we
plan to add Sun and possibly HP Unix soon.
InChI export can be tried most easily using the MarvinSketch applet, for
example at
http://www.chemaxon.com/marvin/doc/dev/example-sketch1.1.html. Draw a
molecule and select Edit >> Source >> Format >> IUPAC InChI.
If someone would like to have Marvin on his local machine, I suggest to
download the Marvin Beans package from http://www.chemaxon.com/marvin/.
(It is free for typical usages: http://www.chemaxon.com/prices.html)
Regards,
Ferenc
From owner-chemistry@ccl.net Wed Nov 9 15:35:00 2005
From: "cristina menziani menziani-$-unimo.it" <owner-chemistry|a|server.ccl.net>
To: CCL
Subject: CCL: call for applications:school of graduate studies
Message-Id: <-29913-051109125008-5424-EB+uiOpNuFoxdqAKjHQr8g|a|server.ccl.net>
X-Original-From: "cristina menziani" <menziani;;unimo.it>
Sent to CCL by: "cristina menziani" [menziani{=}unimo.it]
Universit degli Studi di Modena e Reggio Emilia
School of graduate studies
Multiscale Modelling, Computational Simulations and Characterization in Material and Life Sciences
http://multiscale-school.unimore.it
The School is aimed at providing students with a sound working knowledge of modern mathematical, computational and statistical modelling methods and algorithms as well as innovative experimental techniques for the characterization of complex systems at a multiscale level. The students will learn to apply this knowledge both in the field of material and life sciences working in multi-disciplinary well-integrated teams that emphasize the benefit of coordinated, iterative interactions between specialists in modelling/simulation and experimentalists.
Topics in material and life sciences. Combinatorial and Numerical Algorithms, Computer Graphics, Chemo- and Bio-informatics, Experimental characterization of structures and properties, Human Computer Interface, Mathematical and computational Modelling, Neuroimaging, Statistical Modelling and Chemometrics.
Doctoral Program This is a 3 years full-time course that includes introductory, basic and elective courses, seminars, tutorials, computer and experimental laboratory sessions and project work to produce a final dissertation on original themes of high standard in the international scientific framework. Stages in qualified research institutes in Italy and abroad are part of the student preparation as well.
Possible positions achieved by graduated doctors. Students following this multi-disciplinary training will acquire the mathematical skills, chemical, engineering and biological insight, computational and experimental know-how necessary for tackling real-world problems. They will therefore be highly adaptable, with great employment prospects.
Entry requirements. A second class honours degree or equivalent in a science, biotechnology, medicinal chemistry, medical or engineering subject. Admission is granted on a competitive basis. A Commission examines the CVs of the candidates and evaluates, in an interview (in Italian or English), their abilities to carry out research. Please refer to the Announcement published in the web site http://multiscale-school.unimore.it
Scholarships The School awards 6 scholarships on a merit basis, two of which are reserved for candidates from universities other than the funding institution. Each scholarship is for about Euro 10.500 per year plus School tuition fees. The study grant is increased by 50% per month (for a maximum of 18 months) for time spent by the student at institutions abroad. For students who do not hold a scholarship, the tuition and registration fees amount to about Euro 1000 per year, depending on the income.
Deadlines for application The notice of the competitive examination for the Doctoral Programs is issued Between October and November together with the number of places and scholarships available. The application for admission (www.unimore.it) must be submitted within 30 days of the published notice. Candidates are evaluated in December - January. The Courses begin on January-February1st.
More info? scmamat*_*unimore.it
Prof. Maria Cristina Menziani
University of Modena and Reggio E.
Department of Chemistry
Via Campi 183
41100 Modena -Italy
Tel: +39-059-2055091
Fax: +39-059-373543
E-mail: menziani*_*unimo.it
From owner-chemistry@ccl.net Wed Nov 9 16:10:01 2005
From: "Steven Kirk steven.kirk.*o*.htu.se" <owner-chemistry*o*server.ccl.net>
To: CCL
Subject: CCL: Ab initio simulations of ice-X
Message-Id: <-29914-051109125718-17541-gb9EHjL0WCtMD5NZ66Sw1w*o*server.ccl.net>
X-Original-From: "Steven Kirk" <steven.kirk#,#htu.se>
Sent to CCL by: "Steven Kirk" [steven.kirk#,#htu.se]
Hello,
I would like to ask if anyone on this list is aware of any ab initio electron structure calculations of the high-pressure ice phase ice-X. This is interesting as it has a Cu_{2}O -type structure, and the hydrogen bonds are centrosymmetric (i.e. the H atom is equidistant from both what would be conventionally regarded as the 'donor' and 'acceptor' O atoms).
I have searched the Phys. Rev. and Nature indices, with no success thus far. I would be grateful for any pointers to literature or web pages of active researchers in this area.
Many thanks in advance,
Steve Kirk
From owner-chemistry@ccl.net Wed Nov 9 18:47:00 2005
From: "Kim Baldridge kimb%%sdsc.edu" <owner-chemistry-.-server.ccl.net>
To: CCL
Subject: CCL: Active site volume and surface exposure
Message-Id: <-29915-051109154149-13428-bpIXV2T4DnZqxEt+U50tGw-.-server.ccl.net>
X-Original-From: Kim Baldridge <kimb*sdsc.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
Date: Wed, 9 Nov 2005 12:01:05 -0800 (PST)
MIME-Version: 1.0
Sent to CCL by: Kim Baldridge [kimb|sdsc.edu]
I think you meant another Kim, if I recall seeing the actual question from
this person. Unfortunately, I can no look up her name since I am at
another computer at home.
--
*******************************************************
Kim Baldridge
Prof. of Theoretical Chemistry, UniZH
Director, Computational Applications, UniZH
Distinguished Scientist, SDSC
Adjunct Prof. Chemistry, UCSD
mail: kimb{}sdsc.edu and kimb{}oci.unizh.ch
http://www.oci.unizh.ch/group.pages/baldridge/site/
*******************************************************
On Wed, 9 Nov 2005, Elaine Meng meng|,|cgl.ucsf.edu wrote:
> Sent to CCL by: Elaine Meng [meng ~ cgl.ucsf.edu]
> Hi Kim,
> The following papers used an RMS distance of interface atoms to
> a least-squares plane (there are many more papers, but these will
> get you started):
>
> Jones and Thornton.
> Prediction of protein-protein interaction sites using patch analysis.
> J Mol Biol. 1997 Sep 12;272(1):133-43.
>
> Chakrabarti and Janin.
> Dissecting protein-protein recognition sites.
> Proteins. 2002 May 15;47(3):334-43.
>
> Another measure I've seen is length to width to depth:
>
> Preissner, Goede, and Frommel.
> Dictionary of interfaces in proteins (DIP).
> Data bank of complementary molecular surface patches.
> J Mol Biol. 1998 Jul 17;280(3):535-50.
>
> Hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D. meng-.-cgl.ucsf.edu
> UCSF Computer Graphics Lab and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> http://www.cgl.ucsf.edu/home/meng/index.html
>
>> Sent to CCL by: Kim Branson [kim.branson(~)gmail.com]
>> -----BEGIN PGP SIGNED MESSAGE-----
>> Hash: SHA1
>>
>>
>> Hi all,
>>
>> I'm currently looking for a method that can determine the volume of an
>> active site and its surface exposure. I'm conducting a validation
>> study
>> on protein-protein interaction inhibitors and i would like to quantify
>> the oft heard expression "protein-protein interfaces are often flat
>> featureless surfaces". I'd like to compare the binding sites to
>> that of
>> other systems, and hopefully examine the relationship between scoring
>> function performance and active site volume/surface exposure.
>>
>> I have a crude metric using the ratio of the volume of the active site
>> to the total solvent accessible surface of my defined binding
>> region. I
>> feel there might be a better way to do this.
>>
>> cheers
>>
>> Kim>
>
>
From owner-chemistry@ccl.net Wed Nov 9 21:47:00 2005
From: "Loan H huynhkl2000 : yahoo.ca" <owner-chemistry*_*server.ccl.net>
To: CCL
Subject: CCL: Drug-polymer interaction, diffusion of drug into polymer
Message-Id: <-29916-051109214350-2812-k9O1BPVCf1+lObylc3KCPg*_*server.ccl.net>
X-Original-From: "Loan H" <huynhkl2000%yahoo.ca>
Sent to CCL by: "Loan H" [huynhkl2000]*[yahoo.ca]
Dear all,
I am studying the simulation of drug-polymer interaction. I would appreciate very much if you could give me some suggestion of any drug-polymer interaction/diffusion simulation papers. So far, I was able to find 5 papers only about drug-polymer interaction/diffusion as listed below.
Thank you very in advance.
[1] Lam, Y.-M. et al. Mesoscale Simulation and cryo-TEM of Nanoscale Drug Delivery Systems. Molecular Simulation (2004) 30 (4), 239247
[2] Poupaerta, J.H. and Couvreur, P. A computationally derived structural model of doxorubicin interacting with oligomeric polyalkylcyanoacrylate in nanoparticles. Journal of Controlled Release (2003) 92, 19-26
[3] Li, J. et al. Prediction of drug solubility in an acrylate adhesive based on the drug-polymer interaction parameter and drug solubility in acetonitrile. Journal of Controlled Release (2002) 83, 211-221
[4] Li, T. et al. Computer simulation of molecular diffusion in amorphous polymers. J.Control.Release (1997) 48, 57.
From owner-chemistry@ccl.net Wed Nov 9 22:21:01 2005
From: "Wei David Deng weidavid.deng*yale.edu" <owner-chemistry{=}server.ccl.net>
To: CCL
Subject: CCL:G: Multi-step ONIOM
Message-Id: <-29917-051106230120-61-i40jeT/OX3HJDJdG3YscMw{=}server.ccl.net>
X-Original-From: Wei David Deng <weidavid.deng_-_yale.edu>
Date: Wed, 09 Nov 2005 12:07:11 -0500
Sent to CCL by: Wei David Deng [weidavid.deng===yale.edu]
There are at least two parts are wrong. On the first step, you didn't
specify the link atom and where the hydrogen should be put in the model
system. You need to add "H" at the end of the chloride input.
On the second step, you already said "geom=check", then you shouldn't
enter the H and L levels again. It will automatic extract from the
checkpoint file.
I am attaching my input below. I hope this works in your system, since I
am using a later version of Gaussian.
Sincerely
David Deng
=================================================
%Chk=NaCl
#T oniom(hf/6-31g(d):hf/3-21g*) sp
Title Card Required
0 1
Na
Cl 1 2.000 L H
--Link1--
%Chk=NaCl
#T ONIOM(HF/6-311+G(d,p):HF/6-31G(d)) SP Geom=Check Guess=Read
NaCl SinglePoint-2 Na(High) Cl(Low)
0 1
=====================================
Wei David Deng wrote:
>
> Sent to CCL by: "Telkuni Tsuru" [telkuni]-[venus.dti.ne.jp]
> Hello, CCLers.
>
> I like to ask the description of multi-step ONIOM job on Gaussian98W.
> For example, the following input is correct?
>
> ======= input ========
> %Chk=NaCl
>
> #T ONIOM(HF/6-31G(d):HF/3-21G(d)) SP
>
> NaCl SinglePoint-1 Na(High) Cl(Low)
>
> 0,1 0,1
> Na 2.000000 0.000000 0.000000 H
> Cl 0.000000 0.000000 0.000000 L
>
> --Link1--
> %Chk=NaCl
>
> #T ONIOM(HF/6-311+G(d,p):HF/6-31G(d)) SP Geom=Check Guess=Read
>
> NaCl SinglePoint-2 Na(High) Cl(Low)
>
> 0,1 0,1
> Na H
> Cl L
>
> ======= end of input =======
>
> If you don't mind, please point out the wrong part and teach me correct
> description.
> Any responses I'll appreciate. I will summarize them and upload to this ML.
>
>
> Sincerely yours,
> ----------------------------------------------------
> Telkuni Tsuru telkuni:venus.dti.ne.jp
> Bunshi Gijyutu
> [this "venus" means the planet "venus".]>
>
>
>
>
--
Wei Deng (David), Ph.D.
Post-doctoral Researcher
Department of Chemistry, Yale University
225 Prospect St., P.O. Box 208107
New Haven, CT 06520-8107
Tel: (203) 284-2501
Email: weidavid.deng(0)yale.edu
From owner-chemistry@ccl.net Wed Nov 9 22:57:00 2005
From: "Sue L chsue2004-.-yahoo.com" <owner-chemistry**server.ccl.net>
To: CCL
Subject: CCL:G: Question for solvent field calcauation
Message-Id: <-29918-051109221057-17459-/7FbA/XPK+YXQN80/Q18LA**server.ccl.net>
X-Original-From: "Sue L" <chsue2004*o*yahoo.com>
Sent to CCL by: "Sue L" [chsue2004:+:yahoo.com]
Hi,
I run a cpcm (CH3CN) calculation in Gaussian 03 for a molecule with the D2d
symmetry. However, the calculation terminated abnormally with the following
error message.
Using symmetry in molecular cavity generation.
AdVTs1: ISph= 839 is engulfed by JSph= 847 but Ae( 839) is not yet zero!
Error termination via Lnk1e in /fs/home/app/g03c02/g03/l301.exe
I found that there is a NOSYMMCAV keyword from Gaussian manual, which allows the calculation not imposing the molecular symmetry to the cavity. SymmCav is the default. I run a cpcm calulation by using NOSYMMCAV keyword. The calculation normally terminated. However, I found the following warning messages in the output.
Warning! D(1802,1954)=0.40657557D+02 is big!
D(1802,1802)=0.27113016D+02 D(1954,1954)=0.46253648D+02
Warning! D(1812,1963)=0.40657557D+02 is big!
D(1812,1812)=0.27113016D+02 D(1963,1963)=0.46253648D+02
Warning! D(1954,1802)=0.40657557D+02 is big!
D(1954,1954)=0.46253648D+02 D(1802,1802)=0.27113016D+02
Warning! D(1963,1812)=0.40657557D+02 is big!
D(1963,1963)=0.46253648D+02 D(1812,1812)=0.27113016D+02
Does anyone know whether the NOSYMMCAV is required in the solvent field calculation for the molecule with symmetry? Also, what are these warning messages corresponding to?
Best regards,
Sue