From owner-chemistry@ccl.net Thu Aug 30 03:26:00 2007
From: "Dr. Alexander Hofmann ah#,#chemie.hu-berlin.de" <owner-chemistry:server.ccl.net>
To: CCL
Subject: CCL: Heterogeneous catalysis in Gaussian
Message-Id: <-35055-070830015136-478-iuhTQn2FpfQCL0g+OMqxjw:server.ccl.net>
X-Original-From: "Dr. Alexander Hofmann" <ah===chemie.hu-berlin.de>
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Sent to CCL by: "Dr. Alexander Hofmann" [ah:-:chemie.hu-berlin.de]
Hello Kass,
welcome to the 3D world!
Kaci Tizi_Ouzou kaci.tiziouzou~!~gmail.com wrote:
> Greetings all,
>
> I am currently working on a problem in which I intend to model a
> chemical reaction (oxydation of CO) catalysed by TiO2. At this point I
> wonder what is the usual procedure to model the catalyst. This is what I
> think to do, but I am willing to explore other routes:
>
Just go for some publications in journals like Phys. Rev. B or Surface
Science. You'll get a good overview.
> [1] Optimize CO alone
>
> [2] Optimize TiO2 alone. In this case, I will consider a single cell of
> TiO2. The problem will of course be how to include the crystal effect. I
> hear that VASP or ABINIT use plane wave basis sets which takes care of
> the crystal effect. ANY COMMENTS?
Here is a compilation:
http://www.psi-k.org/codes.shtml (CP2K is missing)
There are many different flavours around, like plane wave or LCAO,
pseudopotentials or not. I'd suggest to start with plane waves and
pseudo potentials in your case. I personally prefer VASP (licence fee).
If you want to go away with free programs, CPMD, CP2K or DACAPO (CAMPOS)
are surely good choices.
>
> [3] Approach a CO molecule and use a scan to determine the TS. In this
> case, I use the cluster (super cluster) methodology. "CO + TiO2" is my
> cluster.
>
> [4] Question: Once I have the TS, can I say that E(TS) = E(CO) + E(TiO2)
> + E(Ads). Here I am quite lost.
>
Yep. Just the way you calculate interaction energies.
Have fun
Alexander
--
Dr. Alexander Hofmann
Humboldt-Universitaet zu Berlin
Institut fuer Chemie
Arbeitsgruppe Quantenchemie
Post: Unter den Linden 6
10099 Berlin
Visitors: Brook-Taylor-Strasse 2
12489 Berlin
ah chemie.hu-berlin.de
]_[
Tel.: +49-30-2093-7138
Fax.: +49-30-2093-7136
http://www.chemie.hu-berlin.de/ag_sauer/index.html
PGP-Key: wwwkeys.de.pgp.net ID: D9D62D35
From owner-chemistry@ccl.net Thu Aug 30 04:28:01 2007
From: "Ol Ga eurisco1:+:pochta.ru" <owner-chemistry:server.ccl.net>
To: CCL
Subject: CCL:G: To: Thermochemical calculations from Gaussian output file
Message-Id: <-35056-070830042124-10319-c16cNucpV4ro9HKO4ohh7A:server.ccl.net>
X-Original-From: "Ol Ga" <eurisco1]^[pochta.ru>
Date: Thu, 30 Aug 2007 04:21:20 -0400
Sent to CCL by: "Ol Ga" [eurisco1 _ pochta.ru]
Moltran - a program for inspection of results after quantum chemical calculations performed with different quantum chemical packages including Gaussian and GAMESS. It also allows editing of a molecular structure working as a molecular builder. During the molecular editing, you can save or retrieve the molecular fragments to a database and use them later to create more complicated structures. A special feature of MOLTRAN is a possibility to perform various thermodynamical calculations (with a broad variation of model parameters) and taking into account the internal rotations if they are present in the molecule.
Have a look at the Moltran sample screenshots (sample data files creating the screenshots can also be found here).
Moltran Manual http://ichem.unn.ru/Moltran/Moltran.pdf
Download the current version of MOLTRAN (v.2.5, build 820) with Short Manual and UnInstaller (MoltranSetup.exe, zipped to avoid the server restrictions)
http://ichem.unn.ru/Moltran/MoltranSetup.zip
From owner-chemistry@ccl.net Thu Aug 30 07:25:01 2007
From: "Yangsoo Kim vsmember(~)gmail.com" <owner-chemistry[-]server.ccl.net>
To: CCL
Subject: CCL:G: Is it possible to install G03 D.02 on the Linux Machine with Multi-Core & Multi-CPU?
Message-Id: <-35057-070830045226-23997-+SdYsbBu/bN+poyWNO8Zyg[-]server.ccl.net>
X-Original-From: "Yangsoo Kim" <vsmember_-_gmail.com>
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Date: Thu, 30 Aug 2007 16:55:14 +0900
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Sent to CCL by: "Yangsoo Kim" [vsmember===gmail.com]
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Dear CCL members
I'm running G03 on the Linux 64bit Machine (AMD X2 4200+ DualCore CPU & M/B
with Single CPU).
I want to upgrade my computer spec. and construct SMP linux
machine(multi-core).
However I'm wondering It is possible to install G03 D.02 on the Linux
machine with QuadCore CPU.
My computer spec. candicates for upgrading are below.
1) AMD(opteron) Quadcore CPU + M/B with Dual CPU = Total 8 cores
2) AMD(opteron) Quadcore CPU + M/B with Single CPU = Total 4 cores
3) AMD(opteron) Dualcore CPU + M/B with Dual CPU = Total 4 cores
4) INTEL(xeon) Core2quad CPU + M/B with Dual CPU = Total 8 cores
5) INTEL(xeon) Core2quad CPU + M/B with Single CPU = Total 4 cores
6) INTEL(xeon) Core2duo CPU + M/B with Dual CPU = Totla 4 cores
Which combination of CPU and M/B could I select?
If tested and possble, please tell me candidate number...
Or not, recommand me another combination of CPU and M/B.
Great thanks,
Yangsoo Kim
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<p>Dear CCL members</p>
<p>I'm running G03 on the Linux 64bit Machine (AMD X2 4200+ DualCore CPU & M/B with Single CPU).<br>I want to upgrade my computer spec. and construct SMP linux machine(multi-core).<br>However I'm wondering It is possible to install G03
D.02 on the Linux machine with QuadCore CPU.</p>
<p>My computer spec. candicates for upgrading are below.<br>1) AMD(opteron) Quadcore CPU + M/B with Dual CPU = Total 8 cores<br>2) AMD(opteron) Quadcore CPU + M/B with Single CPU = Total 4 cores<br>3) AMD(opteron) Dualcore CPU + M/B with Dual CPU = Total 4 cores
<br>4) INTEL(xeon) Core2quad CPU + M/B with Dual CPU = Total 8 cores<br>5) INTEL(xeon) Core2quad CPU + M/B with Single CPU = Total 4 cores<br>6) INTEL(xeon) Core2duo CPU + M/B with Dual CPU = Totla 4 cores</p>
<p>Which combination of CPU and M/B could I select?<br>If tested and possble, please tell me candidate number...<br>Or not, recommand me another combination of CPU and M/B.</p>
<p>Great thanks,</p>
<p>Yangsoo Kim</p>
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From owner-chemistry@ccl.net Thu Aug 30 08:37:00 2007
From: "Xavier Gallet xgallet{:}nautilusbiotech.com" <owner-chemistry-*-server.ccl.net>
To: CCL
Subject: CCL: Tinker compilation
Message-Id: <-35058-070830083456-12807-KKrAk8pAnP9lCZoZ9UnCWw-*-server.ccl.net>
X-Original-From: "Xavier Gallet" <xgallet,,nautilusbiotech.com>
Date: Thu, 30 Aug 2007 08:34:53 -0400
Sent to CCL by: "Xavier Gallet" [xgallet|*|nautilusbiotech.com]
Dear CCLers,
I'd like to recompile the Tinker suite under Windows after modification of the maxatm value.
I used compile.make, library.make and link.make files, respectively using the g77 Fortran compiler of Cygwin.
The first file runs correctly. But the library.make file gave the following error:
"ar: libtinker.a: File format not recognized"
Please, can you suggest me some solutions ?
Thank you in advance,
Xavier
From owner-chemistry@ccl.net Thu Aug 30 14:02:01 2007
From: "Shrinwantu Pal paul|,|jncasr.ac.in" <owner-chemistry^^server.ccl.net>
To: CCL
Subject: CCL: Heterogeneous catalysis in Gaussian
Message-Id: <-35059-070830050751-30133-iOp7WLDunAWG1bU8y4Dvig^^server.ccl.net>
X-Original-From: "Shrinwantu Pal" <paul!^!jncasr.ac.in>
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Date: Thu, 30 Aug 2007 14:45:21 +0530 (IST)
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Sent to CCL by: "Shrinwantu Pal" [paul!=!jncasr.ac.in]
Hi ,
ab init and vasp sure do plane wave basis set calculations for infinite
systems.
however u can use siesta also. it is freely downloadable.
also to do this u need to download (or generate) pseudo potential files
for Ti and O.
See documentation. Once u have the structure, import it to do a
local(small) calculation as to how the systems docks onto the catlyst, as
in ur case is TiO2.
Best of luck..
S.P
JNCASR
India
From owner-chemistry@ccl.net Thu Aug 30 14:37:00 2007
From: "Alfredo Mayall Simas simas###ufpe.br" <owner-chemistry:server.ccl.net>
To: CCL
Subject: CCL: Replacing PM3 with RM1
Message-Id: <-35060-070830143023-16664-cMw7IeFldX/VvJnlzQbL5w:server.ccl.net>
X-Original-From: "Alfredo Mayall Simas" <simas\a/ufpe.br>
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Date: Thu, 30 Aug 2007 15:30:22 -0300
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Sent to CCL by: "Alfredo Mayall Simas" [simas(_)ufpe.br]
This is a multi-part message in MIME format.
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Dear Sina,
Thank you for your interest in the RM1 model.
Answering your questions, please note that parameters are not =
interchangeable among different semiempirical methods. Mixing parameters =
> from different methods will only lead to unstable results, mostly very =
innacurate.
Hence, if you use parameters designed for AM1 in RM1, the results will =
likely be unreliable, at times random - seldom good, most times bad.
Thus, calculations with mixed parameters cannot be trusted. The advice =
by John McKelvey, reinforced by Gustavo Seabra, is truly valid.
When you say that "However all the replacements I have seen are between =
AM1 and RM1", actually, what you have probably been seeing is =
implementation of RM1 in a software which already has AM1.=20
That is possible (and is very easy to be carried out) because the =
equations in both AM1 and RM1 are identical: RM1 differs from AM1 only =
in the values of the parameters.
But after replacing the AM1 parameters with the RM1 ones, the =
calculations are no longer AM1. Indeed they then become RM1 calculations =
only, with no mixing of parameters involved.
What you need, for your specific work on chlorophylls, are RM1 =
parameters for Mg. However, I am sorry to say that they are not yet =
available - but we are carrying out research in that direction.
I am very glad to hear from you that RM1 has been shown to perform =
better for the types of biomolecules you are working on.
More details on the RM1 model can be found at =
http://www.rm1.sparkle.pro.br
Sincerely yours,
Alfredo Mayall Simas
----------------------------------------------------------
Departamento de Qu=EDmica Fundamental
Universidade Federal de Pernambuco
Recife, PE, Brasil
----------------------------------------------------------
But I think the difference is (as someone told me) the equations in RM1 =
and AM1 are the same where is in PM3 there are some differences. Onyl =
problem here is that those MG parameters I found were generated with AM1 =
parameters which also include interractions with the "old" N parameters. =
But still substitutin those MG parameters into RM1 seems to give good =
results.=20
On 8/29/07, Gustavo Seabra gustavo.seabra*_*gmail.com < =
owner-chemistry_._ccl.net> wrote:=20
Sent to CCL by: "Gustavo Seabra" [gustavo.seabra()gmail.com]
On 8/29/07, Sina T=FCreli sinatureli..gmail.com <owner-chemistry:_: =
ccl.net> wrote:
> Thanks for the advice, I have found this=20
>
> http://gepard.bioinformatik.uni-saarland.de/people/hutter/mgam1.html =
>
> which is a work to place a MG parameter in AM1 (so I suppose it =
should work=20
> with RM1). I have found the files that are used for giving the =
paramteres in
> spartan. I am now replacing them all to see if they give good =
results.
Just a note... RM1 is a "re-parametrization" of AM1, as is PM3. In the =
end, it is a different semi-empirical method and, in principle, John
McKelvey's advice is still valid here.
> On the other hand can mopac do geometry optimizations? Thanks...
It should...
Gustavo.
----- Original Message -----=20
From: Sina T=FCreli sinatureli..gmail.com=20
Sent: Wednesday, August 29, 2007 12:53 PM
Subject: CCL: Placing RM1 parameters to PM3
Thanks for the advice, I have found this
http://gepard.bioinformatik.uni-saarland.de/people/hutter/mgam1.html
which is a work to place a MG parameter in AM1 (so I suppose it should =
work with RM1). I have found the files that are used for giving the =
paramteres in spartan. I am now replacing them all to see if they give =
good results.=20
=20
On the other hand can mopac do geometry optimizations? Thanks...
----- Original Message -----=20
From: John McKelvey jmmckel-$-gmail.com=20
Sent: Wednesday, August 29, 2007 10:58 AM
Subject: CCL: Placing RM1 parameters to PM3
One should be careful replacing a single element's parameters from one =
parameter set with that from another. I do not know if it is possible =
to replace parameetrs in Spartan. =20
On the other hand, academeic researchers can get the latest MOPAC from =
Jimmy Stewart for no cost, and this contains RM1, and is _extremely_ =
efficient. [google "MRMOPAC" ]=20
Cheers,
John McKelvey
Or in another point of view, will adding MG parameters into a RM1 or AM1 =
parameters file work?
On 8/29/07, Sina T reli sinatureli%x%gmail.com < =
owner-chemistry]^[ccl.net> wrote:=20
Sent to CCL by: "Sina T reli" [sinatureli],[ gmail.com]
Greetings,
I am working with biomolecules using spartan 04 and I would like to =
update my se methods to RM1 which has been shown to perform better for =
certain types of biomolecules (one is partially which I am working on). =
I have seen people replacing parameters in AM1 with those in RM1. But =
since the molecule I am working with contains MG, I need to use the PM3 =
method. I am wondering, will just replacing the paramters in PM3 with =
those in RM1 is likely to produce a good result? Because all the =
replacements I have seen is between AM1-RM1=20
Thanks,
Sina
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<BODY bgColor=3D#ffffff>
<DIV><FONT face=3DArial size=3D2>Dear Sina,</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>Thank you for your interest in the RM1=20
model.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>Answering your questions, please note =
that=20
parameters are not interchangeable among different semiempirical =
methods.=20
</FONT><FONT face=3DArial size=3D2>Mixing parameters from different =
methods will=20
only lead to unstable results, mostly very innacurate.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2><FONT face=3DArial =
size=3D2></FONT></FONT> </DIV>
<DIV><FONT><FONT face=3DArial size=3D2>Hence, if you use parameters =
designed for AM1=20
in RM1, the results will likely be unreliable, at =
times random=20
- seldom good, most times bad.</DIV>
<DIV></FONT></FONT><FONT></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>Thus, calculations with mixed =
parameters cannot be=20
trusted. The advice by John McKelvey, reinforced by Gustavo=20
Seabra, is truly valid.</FONT></DIV>
<DIV><FONT><FONT face=3DArial size=3D2></FONT> </DIV></FONT><FONT =
face=3DArial=20
size=3D2></FONT>
<DIV><FONT face=3DArial size=3D2>When you say that "However all the =
replacements I=20
have seen are between AM1 and RM1", actually, what you have =
probably=20
been seeing is implementation of RM1 in a software which already =
has AM1.=20
</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>That is possible (and is very easy to =
be carried=20
out) because the equations in both AM1 and RM1 are identical: RM1 =
differs from=20
AM1 only in the values of the parameters.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>But after replacing the AM1 parameters =
with the RM1=20
ones, the calculations are no longer AM1. Indeed they then=20
become RM1 calculations only, with no mixing of parameters=20
involved.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2><FONT face=3DArial =
size=3D2></FONT> </DIV>
<DIV>What you need, for your specific work on chlorophylls, are RM1 =
parameters=20
for Mg. However, I am sorry to say that they are not yet available =
- but we=20
are carrying out research in that direction.</FONT></DIV><FONT =
face=3DArial=20
size=3D2>
<DIV><FONT face=3DArial size=3D2><FONT face=3D"Times New Roman" =
size=3D3><FONT=20
face=3DArial size=3D2></FONT> </DIV></FONT></FONT></FONT>
<DIV><FONT face=3DArial size=3D2>
<DIV><FONT face=3DArial size=3D2>I am very glad to hear from you that =
RM1 has been=20
shown to perform better for the types of biomolecules you are =
working=20
on.</FONT></DIV></FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>More details on the RM1 model can be =
found at <A=20
href=3D"http://www.rm1.sparkle.pro.br">http://www.rm1.sparkle.pro.br</A><=
/FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>Sincerely yours,</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>Alfredo Mayall Simas</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial=20
size=3D2>----------------------------------------------------------</FONT=
></DIV>
<DIV><FONT face=3DArial size=3D2>Departamento de Qu=EDmica =
Fundamental</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>Universidade Federal de =
Pernambuco</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>Recife, PE, Brasil</FONT></DIV>
<DIV><FONT face=3DArial=20
size=3D2>----------------------------------------------------------</FONT=
></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2><FONT face=3D"Times New Roman" =
size=3D3>But I think the=20
difference is (as someone told me) the equations in RM1 and AM1 are the =
same=20
where is in PM3 there are some differences. Onyl problem here is that =
those MG=20
parameters I found were generated with AM1 parameters which also include =
interractions with the "old" N parameters. But still substitutin those =
MG=20
parameters into RM1 seems to give good results. <BR><BR></FONT>
<DIV><SPAN class=3Dgmail_quote>On 8/29/07, <B =
class=3Dgmail_sendername>Gustavo=20
Seabra gustavo.seabra*_*gmail.com</B> <<A=20
onclick=3D"return top.js.OpenExtLink(window,event,this)" href=3D"" =
target=3D_blank>=20
owner-chemistry_._ccl.net</A>> wrote:</SPAN>=20
<BLOCKQUOTE class=3Dgmail_quote=20
style=3D"PADDING-LEFT: 1ex; MARGIN: 0pt 0pt 0pt 0.8ex; BORDER-LEFT: =
rgb(204,204,204) 1px solid"><BR>Sent=20
to CCL by: "Gustavo Seabra" [gustavo.seabra()gmail.com]<BR>On 8/29/07, =
Sina=20
T=FCreli sinatureli..gmail.com <owner-chemistry:_:<A=20
onclick=3D"return top.js.OpenExtLink(window,event,this)" href=3D"" =
target=3D_blank>=20
ccl.net</A>> wrote:<BR>> Thanks for the advice, I have found =
this=20
<BR>><BR>> <A onclick=3D"return =
top.js.OpenExtLink(window,event,this)"=20
href=3D""=20
=
target=3D_blank>http://gepard.bioinformatik.uni-saarland.de/people/hutter=
/mgam1.html=20
</A><BR>><BR>> which is a work to place a MG parameter in AM1 =
(so I=20
suppose it should work <BR>> with RM1). I have found the files that =
are=20
used for giving the paramteres in<BR>> spartan. I am now replacing =
them all=20
to see if they give good results.<BR><BR>Just a note... RM1 is a=20
"re-parametrization" of AM1, as is PM3. In the <BR>end, it is a =
different=20
semi-empirical method and, in principle, John<BR>McKelvey's advice is =
still=20
valid here.<BR><BR>> On the other hand can mopac do geometry =
optimizations?=20
Thanks...<BR><BR>It should...<BR><BR>Gustavo.<BR>
<DIV style=3D"FONT: 10pt arial">----- Original Message -----=20
<DIV style=3D"BACKGROUND: #e4e4e4; font-color: black"><B>From:</B> <A=20
title=3Downer-chemistry*ccl.net =
href=3D"mailto:owner-chemistry*ccl.net">Sina=20
T=FCreli sinatureli..gmail.com</A> </DIV>
<DIV><B>Sent:</B> Wednesday, August 29, 2007 12:53 PM</DIV>
<DIV><B>Subject:</B> CCL: Placing RM1 parameters to PM3</DIV></DIV>
<DIV><BR></DIV>Thanks for the advice, I have found this<BR><BR><A=20
=
href=3D"http://gepard.bioinformatik.uni-saarland.de/people/hutter/mgam1.h=
tml">http://gepard.bioinformatik.uni-saarland.de/people/hutter/mgam1.html=
</A><BR><BR>which=20
is a work to place a MG parameter in AM1 (so I suppose it should work =
with=20
RM1). I have found the files that are used for giving the paramteres =
in=20
spartan. I am now replacing them all to see if they give good results. =
<BR> <BR><BR>On the other hand can mopac do geometry =
optimizations?=20
Thanks...<BR><BR>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV style=3D"FONT: 10pt arial">----- Original Message -----=20
<DIV style=3D"BACKGROUND: #e4e4e4; font-color: black"><B>From:</B> <A=20
title=3Downer-chemistry*ccl.net =
href=3D"mailto:owner-chemistry*ccl.net">John=20
McKelvey jmmckel-$-gmail.com</A> </DIV>
<DIV><B>Sent:</B> Wednesday, August 29, 2007 10:58 AM</DIV>
<DIV><B>Subject:</B> CCL: Placing RM1 parameters to PM3</DIV></DIV>
<DIV><BR></DIV>One should be careful replacing a single element's =
parameters=20
from one parameter set with that from another. I do not know if =
it is=20
possible to replace parameetrs in Spartan. <BR><BR>On the other =
hand,=20
academeic researchers can get the latest MOPAC from Jimmy Stewart for =
no cost,=20
and this contains RM1, and is _extremely_ efficient. [google "MRMOPAC" =
]=20
<BR><BR>Cheers,<BR><BR>John=20
McKelvey<BR><BR></FONT></BLOCKQUOTE></DIV></DIV><FONT face=3DArial =
size=3D2><FONT=20
face=3D"Times New Roman" size=3D3>Or in another point of view, will =
adding MG=20
parameters into a RM1 or AM1 parameters file work?<BR><BR></FONT>
<DIV><SPAN class=3Dgmail_quote>On 8/29/07, <B =
class=3Dgmail_sendername>Sina T reli=20
sinatureli%x%gmail.com</B> <<A href=3D""> =
owner-chemistry]^[ccl.net</A>>=20
wrote:</SPAN>=20
<BLOCKQUOTE class=3Dgmail_quote=20
style=3D"PADDING-LEFT: 1ex; MARGIN: 0pt 0pt 0pt 0.8ex; BORDER-LEFT: =
rgb(204,204,204) 1px solid"><BR>Sent=20
to CCL by: "Sina T reli" [sinatureli],[ <A=20
href=3D"">gmail.com</A>]<BR>Greetings,<BR><BR>I am working with =
biomolecules=20
using spartan 04 and I would like to update my se methods to RM1 which =
has=20
been shown to perform better for certain types of biomolecules (one is =
partially which I am working on). I have seen people replacing =
parameters in=20
AM1 with those in RM1. But since the molecule I am working with =
contains MG, I=20
need to use the PM3 method. I am wondering, will just replacing the =
paramters=20
in PM3 with those in RM1 is likely to produce a good result? Because =
all the=20
replacements I have seen is between AM1-RM1=20
<BR><BR>Thanks,<BR>Sina<BR></BLOCKQUOTE></DIV></FONT></BODY></HTML>
------=_NextPart_000_00C1_01C7EB1A.ADEC2580--
From owner-chemistry@ccl.net Thu Aug 30 19:53:01 2007
From: "Gustavo A Mercier gustavo.mercier+/-bmc.org" <owner-chemistry() server.ccl.net>
To: CCL
Subject: CCL: Computational Chemistry and Molecular Imaging
Message-Id: <-35061-070830134129-1140-nAxgjRwRFgqwAVWT8rYd0Q() server.ccl.net>
X-Original-From: "Gustavo A Mercier" <gustavo.mercier#%#bmc.org>
Date: Thu, 30 Aug 2007 13:41:25 -0400
Sent to CCL by: "Gustavo A Mercier" [gustavo.mercier===bmc.org]
Hi!
I am interested in the application of computatinal chemistry in the development of molecular imaging agents, and contrast media in general. In the past I did work on a putative MRI contrast agent based on a Manganese Metalloporphyrin.
With the recent introduction of a new journal, 'Contrast Media', database, MICAD, and interest group by the Society of Nuclear Medicine (Molecular Imaging), the time seems right to identify those members of the computational chemistry community whose interest is in the development of molecular imaging agents and contrast media.
My interest is to exchange ideas, and see how we could promote computational chemistry as a means to expedite the development of new molcular imaging agents and contrast media.
It seems to me that even within the chemistry community, this endeavor remains a small fraction of the work done by computational chemists. It also seems relatively unknown among the larger radiology/nuclear medicine departments that work on developing such agents.
I am sending this e-mail to the CCL community in the hopes of compiling a list of individuals with interest in this field. If you would like to start a special interest group (for now simple exchange of e-mail addresses), please let me know.
Thank you for your time!
--
Gustavo A. Mercier, Jr. MD,PhD
Boston Medical Center
Radiology - Nuclear Medicine
gamercier::yahoo.com (preferred e-mail address)
Gustavo.Mercier::bmc.org
gumercie::bu.edu
From owner-chemistry@ccl.net Thu Aug 30 20:28:01 2007
From: "John McKelvey jmmckel|gmail.com" <owner-chemistry\a/server.ccl.net>
To: CCL
Subject: CCL: Replacing PM3 with RM1
Message-Id: <-35062-070830191003-19568-Dg3LNOHK+IFLRCrSp3G7HQ\a/server.ccl.net>
X-Original-From: "John McKelvey" <jmmckel|,|gmail.com>
Content-Type: multipart/alternative;
boundary="----=_Part_8043_27776061.1188506885217"
Date: Thu, 30 Aug 2007 16:48:05 -0400
MIME-Version: 1.0
Sent to CCL by: "John McKelvey" [jmmckel.\a/.gmail.com]
------=_Part_8043_27776061.1188506885217
Content-Type: text/plain; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable
Content-Disposition: inline
Why not try PM6 in the latest MOPAC [V7.2] ? I believe in has parameters
for H through I, probably with the exception on the rare fases.
Cheers,
John McKelvey
On 8/30/07, Alfredo Mayall Simas simas###ufpe.br <owner-chemistry\a/ccl.net>
wrote:
>
> Dear Sina,
>
> Thank you for your interest in the RM1 model.
>
> Answering your questions, please note that parameters are not
> interchangeable among different semiempirical methods. Mixing parameters
> from different methods will only lead to unstable results, mostly very
> innacurate.
>
> Hence, if you use parameters designed for AM1 in RM1, the results will
> likely be unreliable, at times random - seldom good, most times bad.
>
> Thus, calculations with mixed parameters cannot be trusted. The advice by
> John McKelvey, reinforced by Gustavo Seabra, is truly valid.
>
> When you say that "However all the replacements I have seen are between
> AM1 and RM1", actually, what you have probably been seeing is implementat=
ion
> of RM1 in a software which already has AM1.
> That is possible (and is very easy to be carried out) because the
> equations in both AM1 and RM1 are identical: RM1 differs from AM1 only in
> the values of the parameters.
> But after replacing the AM1 parameters with the RM1 ones, the calculation=
s
> are no longer AM1. Indeed they then become RM1 calculations only, with no
> mixing of parameters involved.
>
> What you need, for your specific work on chlorophylls, are RM1 parameters
> for Mg. However, I am sorry to say that they are not yet available - but =
we
> are carrying out research in that direction.
>
> I am very glad to hear from you that RM1 has been shown to perform bette=
r
> for the types of biomolecules you are working on.
>
> More details on the RM1 model can be found at
> http://www.rm1.sparkle.pro.br
>
> Sincerely yours,
> Alfredo Mayall Simas
>
> ----------------------------------------------------------
> Departamento de Qu=EDmica Fundamental
> Universidade Federal de Pernambuco
> Recife, PE, Brasil
> ----------------------------------------------------------
>
> But I think the difference is (as someone told me) the equations in RM1
> and AM1 are the same where is in PM3 there are some differences. Onyl
> problem here is that those MG parameters I found were generated with AM1
> parameters which also include interractions with the "old" N parameters. =
But
> still substitutin those MG parameters into RM1 seems to give good results=
.
>
> On 8/29/07, Gustavo Seabra gustavo.seabra*_*gmail.com <owner-chemistry_._=
ccl.net>
> wrote:
> >
> >
> > Sent to CCL by: "Gustavo Seabra" [gustavo.seabra()gmail.com]
> > On 8/29/07, Sina T=FCreli sinatureli..gmail.com <owner-chemistry:_:ccl.=
net>
> > wrote:
> > > Thanks for the advice, I have found this
> > >
> > > http://gepard.bioinformatik.uni-saarland.de/people/hutter/mgam1.html
> > >
> > > which is a work to place a MG parameter in AM1 (so I suppose it shoul=
d
> > work
> > > with RM1). I have found the files that are used for giving the
> > paramteres in
> > > spartan. I am now replacing them all to see if they give good results=
.
> >
> > Just a note... RM1 is a "re-parametrization" of AM1, as is PM3. In the
> > end, it is a different semi-empirical method and, in principle, John
> > McKelvey's advice is still valid here.
> >
> > > On the other hand can mopac do geometry optimizations? Thanks...
> >
> > It should...
> >
> > Gustavo.
> > ----- Original Message ----- *From:* Sina T=FCreli sinatureli..gmail.co=
m<owner-chemistry-$-ccl.net>
> > *Sent:* Wednesday, August 29, 2007 12:53 PM
> > *Subject:* CCL: Placing RM1 parameters to PM3
> >
> > Thanks for the advice, I have found this
> >
> > http://gepard.bioinformatik.uni-saarland.de/people/hutter/mgam1.html
> >
> > which is a work to place a MG parameter in AM1 (so I suppose it should
> > work with RM1). I have found the files that are used for giving the
> > paramteres in spartan. I am now replacing them all to see if they give =
good
> > results.
> >
> >
> > On the other hand can mopac do geometry optimizations? Thanks...
> >
> >
> > ----- Original Message ----- *From:* John McKelvey jmmckel-$-gmail.com=
<owner-chemistry-$-ccl.net>
> > *Sent:* Wednesday, August 29, 2007 10:58 AM
> > *Subject:* CCL: Placing RM1 parameters to PM3
> >
> > One should be careful replacing a single element's parameters from one
> > parameter set with that from another. I do not know if it is possible =
to
> > replace parameetrs in Spartan.
> >
> > On the other hand, academeic researchers can get the latest MOPAC from
> > Jimmy Stewart for no cost, and this contains RM1, and is _extremely_
> > efficient. [google "MRMOPAC" ]
> >
> > Cheers,
> >
> > John McKelvey
> >
> > Or in another point of view, will adding MG parameters into a RM1 or AM=
1
> parameters file work?
>
> On 8/29/07, Sina T reli sinatureli%x%gmail.com < owner-chemistry]^[ccl.ne=
t>
> wrote:
> >
> >
> > Sent to CCL by: "Sina T reli" [sinatureli],[ gmail.com]
> > Greetings,
> >
> > I am working with biomolecules using spartan 04 and I would like to
> > update my se methods to RM1 which has been shown to perform better for
> > certain types of biomolecules (one is partially which I am working on).=
I
> > have seen people replacing parameters in AM1 with those in RM1. But sin=
ce
> > the molecule I am working with contains MG, I need to use the PM3 metho=
d. I
> > am wondering, will just replacing the paramters in PM3 with those in RM=
1 is
> > likely to produce a good result? Because all the replacements I have se=
en is
> > between AM1-RM1
> >
> > Thanks,
> > Sina
> >
>
------=_Part_8043_27776061.1188506885217
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable
Content-Disposition: inline
Why not try PM6 in the latest MOPAC [V7.2] ? I believe in has p=
arameters for H through I, probably with the exception on the rare fases.<b=
r><br>Cheers,<br><br>John McKelvey<br><br><div><span class=3D"gmail_quote">=
On 8/30/07,=20
<b class=3D"gmail_sendername">Alfredo Mayall Simas simas###ufpe.br</b> <=
<a href=3D"mailto:owner-chemistry\a/ccl.net">owner-chemistry\a/ccl.net</a>> =
wrote:</span><blockquote class=3D"gmail_quote" style=3D"border-left: 1px so=
lid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div bgcolor=3D"#ffffff">
<div><font face=3D"Arial" size=3D"2">Dear Sina,</font></div>
<div><font face=3D"Arial" size=3D"2"></font> </div>
<div><font face=3D"Arial" size=3D"2">Thank you for your interest in the RM1=
=20
model.</font></div>
<div><font face=3D"Arial" size=3D"2"></font> </div>
<div><font face=3D"Arial" size=3D"2">Answering your questions, please note =
that=20
parameters are not interchangeable among different semiempirical metho=
ds.=20
</font><font face=3D"Arial" size=3D"2">Mixing parameters from different met=
hods will=20
only lead to unstable results, mostly very innacurate.</font></div>
<div><font face=3D"Arial" size=3D"2"><font face=3D"Arial" size=3D"2"></font=
></font> </div>
<div><font><font face=3D"Arial" size=3D"2">Hence, if you use parameters des=
igned for AM1=20
in RM1, the results will likely be unreliable, at times rand=
om=20
- seldom good, most times bad.</font></font></div>
<div><font></font> </div>
<div><font face=3D"Arial" size=3D"2">Thus, calculations with mixed paramete=
rs cannot be=20
trusted. The advice by John McKelvey, reinforced by Gustavo=20
Seabra, is truly valid.</font></div>
<div><font><font face=3D"Arial" size=3D"2"></font> </font></div><font =
face=3D"Arial" size=3D"2"></font>
<div><font face=3D"Arial" size=3D"2">When you say that "However all th=
e replacements I=20
have seen are between AM1 and RM1", actually, what you have =
probably=20
been seeing is implementation of RM1 in a software which already has A=
M1.=20
</font></div>
<div><font face=3D"Arial" size=3D"2">That is possible (and is very easy to =
be carried=20
out) because the equations in both AM1 and RM1 are identical: RM1 differs f=
rom=20
AM1 only in the values of the parameters.</font></div>
<div><font face=3D"Arial" size=3D"2">But after replacing the AM1 parameters=
with the RM1=20
ones, the calculations are no longer AM1. Indeed they then=20
become RM1 calculations only, with no mixing of parameters=20
involved.</font></div>
<div><font face=3D"Arial" size=3D"2"><font face=3D"Arial" size=3D"2"></font=
> </font></div>
<div>What you need, for your specific work on chlorophylls, are RM1 paramet=
ers=20
for Mg. However, I am sorry to say that they are not yet available - b=
ut we=20
are carrying out research in that direction.</div><font face=3D"Arial" size=
=3D"2">
<div><font face=3D"Arial" size=3D"2"><font face=3D"Times New Roman" size=3D=
"3"><font face=3D"Arial" size=3D"2"></font> </font></font></div></font=
>
<div><font face=3D"Arial" size=3D"2">
<div><font face=3D"Arial" size=3D"2">I am very glad to hear from you that R=
M1 has been=20
shown to perform better for the types of biomolecules you are wor=
king=20
on.</font></div></font></div>
<div><font face=3D"Arial" size=3D"2"></font> </div>
<div><font face=3D"Arial" size=3D"2">More details on the RM1 model can be f=
ound at <a href=3D"http://www.rm1.sparkle.pro.br" target=3D"_blank" onclick=
=3D"return top.js.OpenExtLink(window,event,this)">http://www.rm1.sparkle.pr=
o.br</a>
</font></div>
<div><font face=3D"Arial" size=3D"2"></font> </div>
<div><font face=3D"Arial" size=3D"2">Sincerely yours,</font></div>
<div><font face=3D"Arial" size=3D"2">Alfredo Mayall Simas</font></div>
<div><font face=3D"Arial" size=3D"2"></font> </div>
<div><font face=3D"Arial" size=3D"2">--------------------------------------=
--------------------</font></div>
<div><font face=3D"Arial" size=3D"2">Departamento de Qu=EDmica Fundamental<=
/font></div>
<div><font face=3D"Arial" size=3D"2">Universidade Federal de Pernambuco</fo=
nt></div>
<div><font face=3D"Arial" size=3D"2">Recife, PE, Brasil</font></div>
<div><font face=3D"Arial" size=3D"2">--------------------------------------=
--------------------</font></div>
<div><font face=3D"Arial" size=3D"2"></font> </div>
<div><font face=3D"Arial" size=3D"2"><font face=3D"Times New Roman" size=3D=
"3">But I think the=20
difference is (as someone told me) the equations in RM1 and AM1 are the sam=
e=20
where is in PM3 there are some differences. Onyl problem here is that those=
MG=20
parameters I found were generated with AM1 parameters which also include=20
interractions with the "old" N parameters. But still substitutin =
those MG=20
parameters into RM1 seems to give good results. <br><br></font>
</font><div><span class=3D"gmail_quote"><font face=3D"Arial" size=3D"2">On =
8/29/07, <b class=3D"gmail_sendername">Gustavo=20
Seabra gustavo.seabra*_*gmail.com</b> <<a>=20
owner-chemistry_._ccl.net</a>> wrote:</font></span><font face=3D"Arial" =
size=3D"2">=20
</font><blockquote class=3D"gmail_quote" style=3D"border-left: 1px solid rg=
b(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><font face=
=3D"Arial" size=3D"2"><br>Sent=20
to CCL by: "Gustavo Seabra" [gustavo.seabra()gmail.com]<br>On 8=
/29/07, Sina=20
T=FCreli sinatureli..gmail.com <owner-chemistry:_:<a>=20
ccl.net</a>> wrote:<br>> Thanks for the advice, I have found this=
=20
<br>><br>> <a>http://gepard.bioinformatik.uni-saarland.de/people/hu=
tter/mgam1.html=20
</a><br>><br>> which is a work to place a MG parameter in AM1 (so I=
=20
suppose it should work <br>> with RM1). I have found the files that ar=
e=20
used for giving the paramteres in<br>> spartan. I am now replacing the=
m all=20
to see if they give good results.<br><br>Just a note... RM1 is a=20
"re-parametrization" of AM1, as is PM3. In the <br>end, it is a=
different=20
semi-empirical method and, in principle, John<br>McKelvey's advice is=
still=20
valid here.<br><br>> On the other hand can mopac do geometry optimizat=
ions?=20
Thanks...<br><br>It should...<br><br>Gustavo.<br>
</font><div style=3D"font-family: arial; font-style: normal; font-variant=
: normal; font-weight: normal; font-size: 10pt; line-height: normal; font-s=
ize-adjust: none; font-stretch: normal;"><font face=3D"Arial" size=3D"2">--=
--- Original Message -----=20
</font><div style=3D"background: rgb(228, 228, 228) none repeat scroll 0%=
50%; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-init=
ial; -moz-background-inline-policy: -moz-initial;"><font face=3D"Arial" siz=
e=3D"2">
<b>From:</b> <a title=3D"owner-chemistry-$-ccl.net" href=3D"mailto:owner-ch=
emistry-$-ccl.net" target=3D"_blank" onclick=3D"return top.js.OpenExtLink(w=
indow,event,this)">Sina=20
T=FCreli sinatureli..gmail.com</a> </font></div>
<font face=3D"Arial" size=3D"2"> </font><div><font face=3D"Arial" size=3D"=
2"><b>Sent:</b> Wednesday, August 29, 2007 12:53 PM</font></div>
<font face=3D"Arial" size=3D"2"> </font><div><font face=3D"Arial" size=3D"=
2"><b>Subject:</b> CCL: Placing RM1 parameters to PM3</font></div></div>
<font face=3D"Arial" size=3D"2"> </font><div><font face=3D"Arial" size=3D"=
2"><br></font></div><font face=3D"Arial" size=3D"2">Thanks for the advice, =
I have found this<br><br><a href=3D"http://gepard.bioinformatik.uni-saarlan=
d.de/people/hutter/mgam1.html" target=3D"_blank" onclick=3D"return top.js.O=
penExtLink(window,event,this)">
http://gepard.bioinformatik.uni-saarland.de/people/hutter/mgam1.html</a><br=
><br>which=20
is a work to place a MG parameter in AM1 (so I suppose it should work wit=
h=20
RM1). I have found the files that are used for giving the paramteres in=
=20
spartan. I am now replacing them all to see if they give good results.=20
<br> <br><br>On the other hand can mopac do geometry optimizations?=
=20
Thanks...<br><br>
</font><div><font face=3D"Arial" size=3D"2"><font face=3D"Arial" size=3D"=
2"></font> </font></div>
<font face=3D"Arial" size=3D"2"> </font><div style=3D"font-family: arial; =
font-style: normal; font-variant: normal; font-weight: normal; font-size: 1=
0pt; line-height: normal; font-size-adjust: none; font-stretch: normal;"><f=
ont face=3D"Arial" size=3D"2">
----- Original Message -----=20
</font><div style=3D"background: rgb(228, 228, 228) none repeat scroll 0%=
50%; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-init=
ial; -moz-background-inline-policy: -moz-initial;"><font face=3D"Arial" siz=
e=3D"2">
<b>From:</b> <a title=3D"owner-chemistry-$-ccl.net" href=3D"mailto:owner-ch=
emistry-$-ccl.net" target=3D"_blank" onclick=3D"return top.js.OpenExtLink(w=
indow,event,this)">John=20
McKelvey jmmckel-$-gmail.com</a> </font></div>
<font face=3D"Arial" size=3D"2"> </font><div><font face=3D"Arial" size=3D"=
2"><b>Sent:</b> Wednesday, August 29, 2007 10:58 AM</font></div>
<font face=3D"Arial" size=3D"2"> </font><div><font face=3D"Arial" size=3D"=
2"><b>Subject:</b> CCL: Placing RM1 parameters to PM3</font></div></div>
<font face=3D"Arial" size=3D"2"> </font><div><font face=3D"Arial" size=3D"=
2"><br></font></div><font face=3D"Arial" size=3D"2">One should be careful r=
eplacing a single element's parameters=20
from one parameter set with that from another. I do not know if it =
is=20
possible to replace parameetrs in Spartan. <br><br>On the other han=
d,=20
academeic researchers can get the latest MOPAC from Jimmy Stewart for no =
cost,=20
and this contains RM1, and is _extremely_ efficient. [google "MRMOPA=
C" ]=20
<br><br>Cheers,<br><br>John=20
McKelvey<br><br></font></blockquote></div></div></div><font face=3D"Arial" =
size=3D"2"><font face=3D"Times New Roman" size=3D"3">Or in another point of=
view, will adding MG=20
parameters into a RM1 or AM1 parameters file work?<br><br></font>
</font><div><span class=3D"gmail_quote"><font face=3D"Arial" size=3D"2">On =
8/29/07, <b class=3D"gmail_sendername">Sina T reli=20
sinatureli%x%gmail.com</b> <<a> owner-chemistry]^[ccl.net</a>>=20
wrote:</font></span><font face=3D"Arial" size=3D"2">=20
</font><blockquote class=3D"gmail_quote" style=3D"border-left: 1px solid rg=
b(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><font face=
=3D"Arial" size=3D"2"><br>Sent=20
to CCL by: "Sina T reli" [sinatureli],[ <=
a>gmail.com</a>]<br>Greetings,<br><br>I am working with biomolecules=20
using spartan 04 and I would like to update my se methods to RM1 which ha=
s=20
been shown to perform better for certain types of biomolecules (one is=20
partially which I am working on). I have seen people replacing parameters=
in=20
AM1 with those in RM1. But since the molecule I am working with contains =
MG, I=20
need to use the PM3 method. I am wondering, will just replacing the param=
ters=20
in PM3 with those in RM1 is likely to produce a good result? Because all =
the=20
replacements I have seen is between AM1-RM1=20
<br><br>Thanks,<br>Sina<br></font></blockquote></div>
</blockquote></div><br>
------=_Part_8043_27776061.1188506885217--
From owner-chemistry@ccl.net Thu Aug 30 21:50:00 2007
From: "Raji Raji raji_._anal.chem.tohoku.ac.jp" <owner-chemistry!A!server.ccl.net>
To: CCL
Subject: CCL:G: Error termination via Lnk1e in /usr/ap/g03/l914.exe
Message-Id: <-35063-070830214730-20735-np682dmazBtaH+HZ5HzWuw!A!server.ccl.net>
X-Original-From: "Raji Raji" <raji:anal.chem.tohoku.ac.jp>
Date: Thu, 30 Aug 2007 21:47:26 -0400
Sent to CCL by: "Raji Raji" [raji..anal.chem.tohoku.ac.jp]
Dear CCL Members,
My TDDFT calculation on an organic molecule is terminated with an error. Please do find the part of the input and out put files below. It seems the error in the Link commands. I checked in the gaussian manual, it says that the L914.exe corresponds to CI-Singles, RPA and Zindo excited states; SCF stability. But dont know how to solve this problem. Any help will be thankfully acknowledged.
INPUT
------------------------------------------------------------
%Chk=molecule-ex.chk
%NProc=16
%Mem=128Gb
TD(NStates=15, Singlets, Direct) B3LYP/6-311+G(d) SCRF=(CPCM, Solvent=Water)
AmDMPT Excited Singlet state calculation (CPCM-Water)
0 1
------------------------------------------------------------
OUTPUT
------------------------------------------------------------
60 initial guesses have been made.
Convergence on wavefunction: 0.001000000000000
Iteration 1 Dimension 60 NMult 60
CISAX will form 60 AO SS matrices at one time.
Unable to match L and R vectors in BiOrth.
Error termination via Lnk1e in /usr/ap/g03/l914.exe at Thu Aug 30 12:17:23 2007.
Job cpu time: 0 days 2 hours 10 minutes 30.8 seconds.
File lengths (MBytes): RWF= 599 Int= 0 D2E= 0 Chk= 5 Scr= 1
------------------------------------------------------------