From chemistry-request@server.ccl.net Sun Mar  9 07:13:29 2003
Return-Path: <mark@planaria-software.com>
Reply-To: <mark@planaria-software.com>
From: "Mark Thompson" <mark@planaria-software.com>
To: <chemistry@ccl.net>
Cc: <mark@arguslab.com>
Subject: Bugfix for ArgusLab 3.1
Date: Sun, 9 Mar 2003 18:31:05 -0800
Message-ID: <000601c2e6ad$19fce510$0300a8c0@attbi.com>


We have just posted a bugfix version of ArgusLab 3.1 on our website

	http://www.arguslab.com/download_3_0.htm

This release fixes several bugs in the molecule builder/editor and fixes
bugs in saving of ZINDO UV/vis spectroscopic results to the .uv file.

All ArgusLab 3.0 and 3.1 users can download and install this release for
free.

Please let us know if you have any problems, bugs, or other issues with this
release.

Sincerely,
Mark Thompson

=================================
Mark Thompson, Ph.D.
Planaria Software
PO Box 55207
Seattle, WA  98155

http://www.arguslab.com
FAX: 206-440-3305
=================================

From chemistry-request@server.ccl.net Mon Mar 10 04:16:07 2003
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Date: Mon, 10 Mar 2003 11:24:34 +0200
To: chemistry@ccl.net
Subject: Gold 1.2 segfaults on Red Hat 8.0
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The Linux binary of Gold 1.2 segfaults on Red Hat 8.0 systems. I
upgraded from Mandrake 8.2, where Gold runs without problems. The
native compiler on RH 8.0 is GCC 3.2, which, I think, is binary
incompatible with GCC 2.96 (Mdk 8.2). Apparently the libstdc++/libc in
RH 8.0 do not work with Gold, even though I have the libstdc++-compat
package installed. According to GDB, the segfault occurs in
__libc_start_main () from /lib/i686/libc.so.6.

Has anyone managed to run Gold on RH 8.0? Is the upcoming Gold 2.0
going to be compatible with GCC 3.2 -based distributions?

Mikko



From chemistry-request@server.ccl.net Mon Mar 10 06:37:16 2003
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Date: Mon, 10 Mar 2003 11:32:56 +0000 (GMT)
From: Szilveszter Juhos <szilva@ribotargets.com>
To: Mikko Huhtala <mhuhtala@abo.fi>
cc: chemistry@ccl.net
Subject: Re: CCL:Gold 1.2 segfaults on Red Hat 8.0
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On Mon, 10 Mar 2003, Mikko Huhtala wrote:

> native compiler on RH 8.0 is GCC 3.2, which, I think, is binary
> incompatible with GCC 2.96 (Mdk 8.2). Apparently the libstdc++/libc in

Hello, 
If you check http://gcc.gnu.org, there is no such a thing like gcc 2.96 :/ 
It is invented by RH and unfortunatelly have loads of compatibility 
problems. If the compatibility libs are on your system, you can try:

make CC=egcs CXX=egcs++ 

that is still an old version (2.91). Other option is to get a real 
compiler from the gcc website and re-compile it for yourself. Takes some 
time but worth it.

Cheers:
Szilva


From chemistry-request@server.ccl.net Mon Mar 10 07:19:49 2003
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Dear CCLers,

Do anyone know what is the meaning of "primitive fashion" in the following 
link? And, how do these two links differ?
L310 Computes spdf 2-electron integrals in a primitive fashion 
L314 Computes spdf 2-electron integrals

Thanks in advance.

Best Regards, 
Larry


From chemistry-request@server.ccl.net Mon Mar 10 03:48:12 2003
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Date: Mon, 10 Mar 2003 09:48:07 +0100
To: chemistry@ccl.net
Subject: 64-bit RISC machines - SUMMARY
Message-ID: <20030310084806.GA5642@iveta.uochb.cas.cz>
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From: Daniel Svozil <svozil@iveta.uochb.cas.cz>


--pWyiEgJYm5f9v55/
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Hi,

here is the summary of my knowledge about the use (and usefulness) of
64-bit RISC machines in computational chemistry. As the document is
8 pages long, I prepared PDF file that is attached to this e-mail (I
hope it will go through the system). If you have any questions, please
do not hesitate and contact me at svozil@uochb.cas.cz.

Hope you will find the list interesting.

Regards
  Dan

-- 
Daniel Svozil, PhD
Institute of Organic Chemistry and Biochemistry
and Center for Complex Molecular Systems and Biomolecules
http://www.molecular.cz/
Czech Republic

phone: +420-2-20 183 263

[===========================================
  From the CCL editor: jkl@ccl.net

   Due to size, the PDF file is not attached to this message, but placed in CCL
   archive under: 
        http://www.ccl.net/chemistry/resources/overview/ 
   or
        http://www.ccl.net/cca/documents

   Namely: 
        http://www.ccl.net/cca/documents/64-bit_in_CC_summary.pdf 

================================================]

   
From chemistry-request@server.ccl.net Mon Mar 10 11:24:02 2003
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Date: Mon, 10 Mar 2003 08:24:01 -0800 (PST)
From: Konstantin Kudin <konstantin_kudin@yahoo.com>
Subject: Re: CCL:64-bit RISC machines - SUMMARY
To: Daniel Svozil <svozil@iveta.uochb.cas.cz>
Cc: chemistry@ccl.net
In-Reply-To: <20030310084806.GA5642@iveta.uochb.cas.cz>
MIME-Version: 1.0
Content-Type: text/plain; charset=us-ascii

 Daniel

 Good document on 64 bit computing in CC! IMO, it
could benefit substantially if the reasons for going
64 bits were explained more clearly.
 Specifically, it appears that pretty much every 32
bit application on every OS is stuck with the 2Gb RAM
limit (even outside of CC). That is very achievable
with the latest systems. Also, there are usually
limits on the size of temporary files on the hard
drive. Current hard drive sizes far exceed what some
CC applications could address in terms of disk space
in 32 bits.
 Thus, one could expect a pretty significant push from
all vendors/software developers to 64 bits. While x86
32 bit systems have become really competitive with
RISC systems in terms of CPU performance and memory
bandwidth, the addressable memory size is becoming the
major roadblock. Some calculations can't be run in 32
bits simply because the needed RAM and disk space
could not be allocated and addressed on the software
level. It is not a problem to leave a computer running
for a month, but what can one do if enough RAM can't
be allocated due to 32 bit limitations?
 From this perspective the upcoming x86-64 systems
under Linux could provide huge benefit to the CC
community. The addressable RAM and disk could go as
far as the limits of physical RAM and disk space, thus
enabling truly monstrous calculations on really cheap
systems.

 Regards,
 Konstantin

--- Daniel Svozil <svozil@iveta.uochb.cas.cz> wrote:
> Hi,
> 
> here is the summary of my knowledge about the use
> (and usefulness) of
> 64-bit RISC machines in computational chemistry. As
> the document is
> 8 pages long, I prepared PDF file that is attached
> to this e-mail (I
> hope it will go through the system). If you have any
> questions, please
> do not hesitate and contact me at
> svozil@uochb.cas.cz.


__________________________________________________
Do you Yahoo!?
Yahoo! Tax Center - forms, calculators, tips, more
http://taxes.yahoo.com/


From chemistry-request@server.ccl.net Mon Mar 10 14:03:37 2003
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Date: Mon, 10 Mar 2003 20:03:36 +0100
To: chemistry@ccl.net
Subject: 64-bit machines document - where is it?
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From: Daniel Svozil <svozil@iveta.uochb.cas.cz>

Hi,

the PDF document didn't get into CCL list due to its size, it can be
downloaded from:

http://www.ccl.net/cca/documents/64-bit_in_CC_summary.pdf

Regards
  Dan

-- 
Daniel Svozil, PhD
Institute of Organic Chemistry and Biochemistry
and Center for Complex Molecular Systems and Biomolecules
http://www.molecular.cz/
Czech Republic

phone: +420-2-20 183 263

From chemistry-request@server.ccl.net Mon Mar 10 11:40:58 2003
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From: "LEDM (Leonardo De Maria)" <ledm@novozymes.com>
To: "'chemistry@ccl.net'" <chemistry@ccl.net>
Subject: Protein-polysaccharide interactions: CHARMM parameters?
Date: Mon, 10 Mar 2003 17:40:52 +0100
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Hi to everyone,

I am setting up some MD simulations of protein-polysaccharide complexes =
and
I was wandering
if there is a set of parameter for CHARMM to do this. I have already =
found
prof. Brady's new CHARMM
parameters for polysaccharides in solution but they are not useful for =
my
purpose.

Any help from out there?

Bye,

Leonardo De Maria, Ph.D.
Research Scientist
Novozymes A/S
Sm=F8rmosevej 25
2880 Bagsv=E6rd
Denmark

Phone:  +45 44421890
Fax:      +45 44980246

e.mail: ledm@novozymes.com



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<TITLE>Protein-polysaccharide interactions: CHARMM parameters?</TITLE>
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<BODY>

<P><FONT SIZE=3D2 FACE=3D"Arial">Hi to everyone,</FONT>
</P>

<P><FONT SIZE=3D2 FACE=3D"Arial">I am setting up some MD simulations of =
protein-polysaccharide complexes and I was wandering</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">if there is a set of parameter for =
CHARMM to do this. I have already found prof. Brady's new CHARMM</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">parameters for polysaccharides in =
solution but they are not useful for my purpose.</FONT>
</P>

<P><FONT SIZE=3D2 FACE=3D"Arial">Any help from out there?</FONT>
</P>

<P><FONT SIZE=3D2 FACE=3D"Arial">Bye,</FONT>
</P>

<P><FONT SIZE=3D2 FACE=3D"Arial">Leonardo De Maria, Ph.D.</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">Research Scientist</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">Novozymes A/S</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">Sm=F8rmosevej 25</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">2880 Bagsv=E6rd</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">Denmark</FONT>
</P>

<P><FONT SIZE=3D2 FACE=3D"Arial">Phone:&nbsp; +45 44421890</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">Fax:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =
+45</FONT> <FONT SIZE=3D2 FACE=3D"Arial">44980246</FONT>
</P>

<P><FONT SIZE=3D2 FACE=3D"Arial">e.mail: ledm@novozymes.com</FONT>
</P>
<BR>

</BODY>
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From chemistry-request@server.ccl.net Mon Mar 10 16:04:15 2003
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	Mon, 10 Mar 2003 16:04:14 -0500 (EST)
Date: Mon, 10 Mar 2003 16:04:13 -0500 (EST)
From: Jan Labanowski <jkl@ccl.net>
To: chemistry@ccl.net
cc: Jan Labanowski <jkl@ccl.net>
Subject: Prof. Alexander Ovchinnikov dies
Message-ID: <Pine.GSO.4.21.0303101558240.5881-100000@krakow.ccl.net>
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I am reporting with great sadness that Professor Alexander Ovchinnikov
recently died of heart failure.	

Prof. Alexander Anatolievich Ovchinnikow was born on November 11, 1938.
In 1970 he became a professor of Chemical Physics. In 1981 he joined
the Russian Academy of Sciences as a corresponding member. He held
important scientific posts (Karpov Institute of Chemical Physics,
Department of Electronics of Organic Materials at Institute of Chemical
Physics of RAS). After spending some time at the Max-Planck Institute
for Physics of Complex Systems in Dresden, he returned to Moscow
to head the Department of Electronics of Organic Materials at
the Institute of Biochemical Physics of RAS ( http://ibcp.chph.ras.ru/ ).
A memorial service will be held at his Institute at 10:30 am Moscow time,
on Tue, March 11, 2003.

He will be remembered for his friendly and open attitude, always ready
to help and assist. He will be missed by many in the scientific community
as a friend, mentor, and teacher. His knowledge and understanding
are irreplaceable.

He is survived by his wife Marina and his sons.

For me personally, and for all of us who had a chance to know Sasha
and to work with him, it is an unexpected and tragic news...

Jan K. Labanowski
jkl@ccl.net




From chemistry-request@server.ccl.net Mon Mar 10 13:09:34 2003
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From: "Carsten Detering" <detering@u.washington.edu>
To: <chemistry@ccl.net>
Subject: LUDI
Date: Mon, 10 Mar 2003 19:09:30 +0100
Organization: University of Washington
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Hi everybody,

does anybody know a link to a manual or user's guide to Boehm's LUDI?

Thanks in advance,

Carsten

~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Carsten Detering, Ph.D.
University of Washington
Seattle, WA 98195
Fon 206-543-5081
Fax 206-865-8665
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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<DIV><FONT face=3DArial size=3D2>Hi everybody,</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>does anybody know a link to a manual or =
user's=20
guide to Boehm's LUDI?</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>Thanks in advance,</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>Carsten</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>~~~~~~~~~~~~~~~~~~~~~~~~~~~~<BR>Carsten =
Detering,=20
Ph.D.<BR>University of Washington<BR>Seattle, WA 98195<BR>Fon=20
206-543-5081<BR>Fax=20
206-865-8665<BR>~~~~~~~~~~~~~~~~~~~~~~~~~~~~</FONT></DIV></BODY></HTML>

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From chemistry-request@server.ccl.net Mon Mar 10 13:12:12 2003
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Hi, does anyone know where I can get the parameters for Hydantoin or its'
derivatives? Thanks a lot!

Have a good day.

William

-------------------------
William Wei
Faculty of Pharmacy
19 Russell Street
Toronto, ON. M5S 2S2
Tel: 1-416-946-8469
Fax: 1-416-978-8511
Email: william@phm.utoronto.ca
       william.wei@utoronto.ca




From chemistry-request@server.ccl.net Mon Mar 10 11:40:58 2003
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From: "LEDM (Leonardo De Maria)" <ledm@novozymes.com>
To: "'chemistry@ccl.net'" <chemistry@ccl.net>
Subject: Protein-polysaccharide interactions: CHARMM parameters?
Date: Mon, 10 Mar 2003 17:40:52 +0100
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Hi to everyone,

I am setting up some MD simulations of protein-polysaccharide complexes =
and
I was wandering
if there is a set of parameter for CHARMM to do this. I have already =
found
prof. Brady's new CHARMM
parameters for polysaccharides in solution but they are not useful for =
my
purpose.

Any help from out there?

Bye,

Leonardo De Maria, Ph.D.
Research Scientist
Novozymes A/S
Sm=F8rmosevej 25
2880 Bagsv=E6rd
Denmark

Phone:  +45 44421890
Fax:      +45 44980246

e.mail: ledm@novozymes.com



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<BODY>

<P><FONT SIZE=3D2 FACE=3D"Arial">Hi to everyone,</FONT>
</P>

<P><FONT SIZE=3D2 FACE=3D"Arial">I am setting up some MD simulations of =
protein-polysaccharide complexes and I was wandering</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">if there is a set of parameter for =
CHARMM to do this. I have already found prof. Brady's new CHARMM</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">parameters for polysaccharides in =
solution but they are not useful for my purpose.</FONT>
</P>

<P><FONT SIZE=3D2 FACE=3D"Arial">Any help from out there?</FONT>
</P>

<P><FONT SIZE=3D2 FACE=3D"Arial">Bye,</FONT>
</P>

<P><FONT SIZE=3D2 FACE=3D"Arial">Leonardo De Maria, Ph.D.</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">Research Scientist</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">Novozymes A/S</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">Sm=F8rmosevej 25</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">2880 Bagsv=E6rd</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">Denmark</FONT>
</P>

<P><FONT SIZE=3D2 FACE=3D"Arial">Phone:&nbsp; +45 44421890</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">Fax:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =
+45</FONT> <FONT SIZE=3D2 FACE=3D"Arial">44980246</FONT>
</P>

<P><FONT SIZE=3D2 FACE=3D"Arial">e.mail: ledm@novozymes.com</FONT>
</P>
<BR>

</BODY>
</HTML>
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From chemistry-request@server.ccl.net Mon Mar 10 13:09:34 2003
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From: "Carsten Detering" <detering@u.washington.edu>
To: <chemistry@ccl.net>
Subject: LUDI
Date: Mon, 10 Mar 2003 19:09:30 +0100
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Hi everybody,

does anybody know a link to a manual or user's guide to Boehm's LUDI?

Thanks in advance,

Carsten

~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Carsten Detering, Ph.D.
University of Washington
Seattle, WA 98195
Fon 206-543-5081
Fax 206-865-8665
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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<DIV><FONT face=3DArial size=3D2>Hi everybody,</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>does anybody know a link to a manual or =
user's=20
guide to Boehm's LUDI?</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>Thanks in advance,</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>Carsten</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>~~~~~~~~~~~~~~~~~~~~~~~~~~~~<BR>Carsten =
Detering,=20
Ph.D.<BR>University of Washington<BR>Seattle, WA 98195<BR>Fon=20
206-543-5081<BR>Fax=20
206-865-8665<BR>~~~~~~~~~~~~~~~~~~~~~~~~~~~~</FONT></DIV></BODY></HTML>

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From chemistry-request@server.ccl.net Mon Mar 10 13:12:12 2003
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From: "William Wei" <william.wei@utoronto.ca>
To: "CCLers" <CHEMISTRY@ccl.net>,
   "Amber List" <amber@heimdal.compchem.ucsf.edu>
Subject: Parameters for Hyddantoin derivatives?
Date: Mon, 10 Mar 2003 13:13:48 -0500
Message-ID: <MDEIKEJBFAGCDMAAIPIBKEKCCCAA.william.wei@utoronto.ca>
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Hi, does anyone know where I can get the parameters for Hydantoin or its'
derivatives? Thanks a lot!

Have a good day.

William

-------------------------
William Wei
Faculty of Pharmacy
19 Russell Street
Toronto, ON. M5S 2S2
Tel: 1-416-946-8469
Fax: 1-416-978-8511
Email: william@phm.utoronto.ca
       william.wei@utoronto.ca




From chemistry-request@server.ccl.net Mon Mar 10 16:04:15 2003
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	Mon, 10 Mar 2003 16:04:14 -0500 (EST)
Date: Mon, 10 Mar 2003 16:04:13 -0500 (EST)
From: Jan Labanowski <jkl@ccl.net>
To: chemistry@ccl.net
cc: Jan Labanowski <jkl@ccl.net>
Subject: Prof. Alexander Ovchinnikov dies
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I am reporting with great sadness that Professor Alexander Ovchinnikov
recently died of heart failure.	

Prof. Alexander Anatolievich Ovchinnikow was born on November 11, 1938.
In 1970 he became a professor of Chemical Physics. In 1981 he joined
the Russian Academy of Sciences as a corresponding member. He held
important scientific posts (Karpov Institute of Chemical Physics,
Department of Electronics of Organic Materials at Institute of Chemical
Physics of RAS). After spending some time at the Max-Planck Institute
for Physics of Complex Systems in Dresden, he returned to Moscow
to head the Department of Electronics of Organic Materials at
the Institute of Biochemical Physics of RAS ( http://ibcp.chph.ras.ru/ ).
A memorial service will be held at his Institute at 10:30 am Moscow time,
on Tue, March 11, 2003.

He will be remembered for his friendly and open attitude, always ready
to help and assist. He will be missed by many in the scientific community
as a friend, mentor, and teacher. His knowledge and understanding
are irreplaceable.

He is survived by his wife Marina and his sons.

For me personally, and for all of us who had a chance to know Sasha
and to work with him, it is an unexpected and tragic news...

Jan K. Labanowski
jkl@ccl.net




