From chemistry-request@server.ccl.net  Tue Nov  7 15:47:50 2000
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Date: Tue, 07 Nov 2000 15:52:44 -0500
From: elewars <elewars@trentu.ca>
Subject: Re: Number of isomers of alkanes
To: chemistry@ccl.net
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Hello,

There is only a _recursive_ formula: to calc N(n) (the number of isomers N for n
carbons) you have to know N for n-1 carbons. Knowing N for CH4 you can calculate N
for C2H6, C3H8, etc. The mathematics comes from tree theory, a branch of
combinatorial analysis.

E. Lewars
====

dido dido2 wrote:

> Can you tell me the formula for determination number of isomers according to
> number of carbon atoms at alkanes??
> please
> _________________________________________________________________________
> Get Your Private, Free E-mail from MSN Hotmail at http://www.hotmail.com.
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From chemistry-request@server.ccl.net  Tue Nov  7 21:41:47 2000
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Date: Mon, 08 Nov 1999 11:41:29 -0800
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Organization: The Catholic University of Korea
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Hi CCLers...

I compiled GROMACS in my computer but some errors were detected
and only three bynaries were produced.
My computer is SGI IRIX6.2 R5000 (INDY).
I read the Readme.html and tried to compile as it said.
And I tried to correct the R5000 compiled error as Readme, too.

Could you tell me what is wrong...?

Error message was followed...

cc -n32 -r5000 -mips4 -O3 -OPT:IEEE_arithmetic=3 -OPT:rsqrt=ON
-SWP:loop_overhead -INLINE:=ON -LNO:opt=1 -LNO:ou_further=3
-OPT:Olimit=0:roundoff=3:alias=typed -fullwarn -woff 1174  -D_s5k_
-DHAVE_IDENT -D__INLINE_INTRINSICS -DHAVE_STRDUP -D_SGI_
-DHAVE_STRCASECMP -DSIMPLEWATER  -DHAVE_MOTIF -DUSEF/error
...skipping
ld32: ERROR 33: Unresolved text symbol "fftw_hc2hc_backward_generic" --
1st referenced by /usr3/MD/GROMACS/lib/s5k/libfftw.s5k.a(rplanner.o).
ld32: ERROR 33: Unresolved text symbol "fftw_hc2hc_forward_generic" --
1st referenced by /usr3/MD/GROMACS/lib/s5k/libfftw.s5k.a(rplanner.o).
ld32: INFO 60: Output file removed because of error.
make[1]: *** [mdrun] Error 2
make[1]: Leaving directory `/usr3/MD/GROMACS/src/kernel'
make[1]: Entering directory `/usr3/MD/GROMACS/src/tools'
echo "No library in tools"
No library in tools
cc -L/usr3/MD/GROMACS/lib/s5k -n32 -r5000 -mips4  -o g_disre g_disre.o
-Bstatic -lmd.s5k -lgmx.s5k -lfftw.s5k -Bdynamic -lm -lXm -lXt -lX11
ld32: ERROR 33: Unresolved text symbol "fftw_hc2hc_backward_generic" --
1st referenced by /usr3/MD/GROMACS/lib/s5k/libfftw.s5k.a(rplanner.o).
ld32: ERROR 33: Unresolved text symbol "fftw_hc2hc_forward_generic" --
1st referenced by /usr3/MD/GROMACS/lib/s5k/libfftw.s5k.a(rplanner.o).
ld32: INFO 60: Output file removed because of error.
make[1]: *** [g_disre] Error 2
make[1]: Leaving directory `/usr3/MD/GROMACS/src/tools'
make[1]: Entering directory `/usr3/MD/GROMACS/src/ngmx'
echo "No library in ngmx"
No library in ngmx
cc -L/usr3/MD/GROMACS/lib/s5k -n32 -r5000 -mips4  -o ngmx ngmx.o xutil.o
xmb.o x11.o xdlghi.o fgrid.o xdlgitem.o popup.o pulldown.o xdlg.o
manager.o buttons.o nmol.o nleg.o dialogs.o logo.o filter.o molps.o
-lgmx.s5k -lm -lXm -lXt -lX11
cc -L/usr3/MD/GROMACS/lib/s5k -n32 -r5000 -mips4  -o xrama xrama.o
xutil.o xmb.o x11.o xdlghi.o fgrid.o xdlgitem.o popup.o pulldown.o
xdlg.o manager.o buttons.o nmol.o nleg.o dialogs.o logo.o filter.o
molps.o       -lgmx.s5k -lm -lXm -lXt -lX11
cc -L/usr3/MD/GROMACS/lib/s5k -n32 -r5000 -mips4  -o highway highway.o
xutil.o xmb.o x11.o xdlghi.o fgrid.o xdlgitem.o popup.o pulldown.o
xdlg.o manager.o buttons.o nmol.o nleg.o dialogs.o logo.o filter.o
molps.o   -lgmx.s5k -lm -lXm -lXt -lX11
cd /usr3/MD/GROMACS/bin/s5k ; /bin/rm -f  ngmx  xrama  highway
chmod 755  ngmx  xrama  highway
mv  ngmx  xrama  highway /usr3/MD/GROMACS/bin/s5k
make[1]: Leaving directory `/usr3/MD/GROMACS/src/ngmx'
local: Does not exist
make[1]: Entering directory `/usr3/MD/GROMACS/src'
\mkdir -p /usr3/MD/GROMACS/bin/s5k /usr3/MD/GROMACS/lib/s5k;
cd include; /usr3/Util/make-3.79.1/make oclean; cd ..; cd gmxlib;
/usr3/Util/make-3.79.1/make oclean; cd ..; cd mdlib;
/usr3/Util/make-3.79.1/make oclean; cd ..; cd fftw;
/usr3/Util/make-3.79.1/make oclean; cd ..; cd kernel;
/usr3/Util/make-3.79.1/make oclean; cd ..; cd tools;
/usr3/Util/make-3.79.1/make oclean; cd ..; cd ngmx;
/usr3/Util/make-3.79.1/make oclean; cd ..;
make[2]: Entering directory `/usr3/MD/GROMACS/src/include'
rm -f *~ #*#
make[2]: Leaving directory `/usr3/MD/GROMACS/src/include'
make[2]: Entering directory `/usr3/MD/GROMACS/src/gmxlib'
/
...skipping
ld32: ERROR 33: Unresolved text symbol "fftw_hc2hc_backward_generic" --
1st referenced by /usr3/MD/GROMACS/lib/s5k/libfftw.s5k.a(rplanner.o).
ld32: ERROR 33: Unresolved text symbol "fftw_hc2hc_forward_generic" --
1st referenced by /usr3/MD/GROMACS/lib/s5k/libfftw.s5k.a(rplanner.o).
ld32: INFO 60: Output file removed because of error.
make[2]: *** [mdrun] Error 2


Bye...

                                             11. 8 young



--
=================================
Jee-Young Lee
The Catholic University of Korea
Department of Chemistry
Ph.D candidate
TEL. +82-32-3403-674
=================================





From chemistry-request@server.ccl.net  Wed Nov  8 07:27:31 2000
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Hi,

I am looking for the program GRID by Peter Goodford. I found a couple of
answers to the same inquiry in the CCL archives but the information
given there does not seem to be valid anymore.

Specifically, I tried to contact Henrietta Elton at Molecular Discovery
Ltd., but the fax machine with the number +44-993-830966 appears to be
non-existent.

Is the program still available at all? Who should I contact? Am I just
not able to operate a fax machine properly?

Apart from that, are there other (preferably free for academics)
programs around that can be used for similar purposes?

Many thanks in advance!

Karl
 
---------------------------------------------------------------------
Karl Gruber
Institute of Chemistry -- Structural Biology
KFU Graz
Heinrichstrasse 28		  e-mail: karl.gruber@kfunigraz.ac.at
A-8010 Graz			   phone: (+43 316) 380-5483
AUSTRIA				     fax: (+43 316) 380-9850
---------------------------------------------------------------------

From chemistry-request@server.ccl.net  Wed Nov  8 08:48:16 2000
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Date: Wed, 8 Nov 2000 14:53:00 +0100 (CET)
From: Alexander Hofmann <hofmann@aca-berlin.de>
To: chemistry@ccl.net
Subject: MARVIN - examples needed
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Hello together,

is there somebody who has got experience with MARVIN 2.00 (beta 2) and may
provide one (ore more) input example(s)? It seems that the manual example
did not work.

Thank you in advance

Alex



---

Dr. Alexander Hofmann
Institut fuer Angewandte Chemie Berlin-Adlershof e.V.
Richard-Willstaetter-Str. 12

D-12489 Berlin

hofmann@aca-berlin.de

Tel.: +49-30-6392-4408
Fax.: +49-30-6392-4350

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From chemistry-request@server.ccl.net  Wed Nov  8 10:13:05 2000
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Date: Wed, 08 Nov 2000 10:12:41 -0500
From: "Shobe, Dave" <dshobe@sud-chemieinc.com>
Subject: RE: Number of isomers of alkanes
To: "'elewars'" <elewars@trentu.ca>, chemistry@ccl.net
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 <157A51F55AAAD3119CD70008C7B1629D638689@lvlxch01.unitedcatalysts.com>
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Anyone know the recursive formula?  Is it complicated?

--David Shobe
Süd-Chemie Inc.
phone (502) 634-7409
fax     (502) 634-7724
email  dshobe@sud-chemieinc.com



-----Original Message-----
From: elewars [mailto:elewars@trentu.ca]
Sent: Tuesday, November 07, 2000 3:53 PM
To: chemistry@ccl.net
Subject: CCL:Number of isomers of alkanes


Hello,

There is only a _recursive_ formula: to calc N(n) (the number of isomers N
for n
carbons) you have to know N for n-1 carbons. Knowing N for CH4 you can
calculate N
for C2H6, C3H8, etc. The mathematics comes from tree theory, a branch of
combinatorial analysis.

E. Lewars
====

dido dido2 wrote:

> Can you tell me the formula for determination number of isomers according
to
> number of carbon atoms at alkanes??
> please
> _________________________________________________________________________
> Get Your Private, Free E-mail from MSN Hotmail at http://www.hotmail.com.
>
> Share information about yourself, create your own public profile at
> http://profiles.msn.com.
>



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From chemistry-request@server.ccl.net  Wed Nov  8 12:02:39 2000
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Date: Wed, 8 Nov 2000 18:01:42 +0100 (MET)
From: Marcin Krol <mykrol@cyf-kr.edu.pl>
To: <chemistry@ccl.net>
cc: <charmm-bbs@csir.org>
Subject: Diazo dyes in CHARMM
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Dear CCLers,
I want to simulate diazo dyes and their interactions with proteins in
CHARMM using academic, all atom forcefield. I  built RTF file for my
diazo dye and chose atom types that I thought fitted 'well' with my
structure. However, I could not find proper atom types for sulphur in
SO3H- and nitrogen in -N=N- and so on. Moreover, there were 'missing
paramters'. So I used Quanta and got all atom types and
missing paramters given by Parameter Chooser. However, these atom types
and parameters belong to QUANTA_CHARMm forcefield.

Is it safe to take them to academic par22 FF? I'm afraid it isn't.
Maybe someone has parameters for diazo dyes in par22, or maybe someone can tell me how to transform
parameters from CHARMm (Quanta) to CHARMM (academic)?
How can I get parameters in another way?
I know I'm asking a generic question, so I'd be also grateful if you
could refer me to a good book/article about parametrization process for
small ligand molecules.
Thanks in advance
Marcin Krol


From chemistry-request@server.ccl.net  Wed Nov  8 12:58:00 2000
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Date: Wed, 08 Nov 2000 13:02:22 -0500
From: elewars <elewars@trentu.ca>
Subject: FRIEDRICH HUND, LONGUET-HIGGINS
To: chemistry@ccl.net
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2000 Wed Nov 8

Hello,

(I turn to CCL after being unable to find this info' elesewhere):

Where did Friedrich Hund get his doctorate (not his _Habilitation_)?

When and where did Longuet-Higgins die?

Thanks very much.

E. Lewars
=====


From chemistry-request@server.ccl.net  Wed Nov  8 15:06:01 2000
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Date: Wed, 08 Nov 2000 15:03:36 -0500
From: "Curt M. Breneman" <brenec@rpi.edu>
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Dear COMP Chem enthusiasts:

This is just a reminder that the deadline for COMP Division abstract
submissions for the San Diego ACS meeting is coming nearer...(November
13th).

Another Reminder:

ARTIFICIAL INTELLIGENCE IN COMPUTATIONAL CHEMISTRY SYMPOSIUM
  
The ACS Division of Computers in Chemistry is sponsoring a symposium on 
the use of Artificial Intelligence in Computational Chemistry at the 
Spring ACS meeting in San Diego, CA.
  
Presentations covering all uses of machine intelligence in computational 
chemistry will be welcomed, including machine learning, SVM, GA or 
Neural Network model building, Evolutionary Computing, ADME screening or
datamining.  For further information, please contact me at
brenec@rpi.edu.
  
Abstract submission should be made through the ACS OASys system at 
http://oasys.acs.org/oasys.htm
  
Curt Breneman
RPI Chemistry
COMP Treasurer

(p.s. Your submissions are welcome!)

From chemistry-request@server.ccl.net  Wed Nov  8 16:51:21 2000
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CC: Computational Chemistry List <chemistry@server.ccl.net>
Subject: change basis set in G98
References: <200002021631.RAA12248@rs5.thch.uni-bonn.de>
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Hi everybody

Can I use "guess=read" in route when changing basis set for an
atom from one basis set to another? Will that cause any trouble
when G98 read the wavefunction to the current geometry?  For
example:

---first input---
%Chk=first.chk
%Mem=256MB
%nproc=2
# b3lyp/gen opt

0 1
A 0. 0. 0.
B 0. 1. 0.
C 0. 0. 1.

A 0
3-21G
****
B 0
3-21G
****
C 0
3-21G
****


---second input---
%Chk=first.chk
%Mem=256MB
%nproc=2
# b3lyp/gen opt guess=read geom=checkpoint

0 1

A 0
3-21G
****
B 0
6-311G**
****
C 0
3-21G
****

Since 3-21G is different than 6-311G**, will G98 read the
wavefunction right? How guess=read was handled by G98? Can I do
the same thing if I used 6-311G** for B atom first, then in the
second calc. using 3-21G?

Many thanks.

huajun

From chemistry-request@server.ccl.net  Wed Nov  8 20:28:18 2000
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Cc: "Computational Chemistry List" <chemistry@server.ccl.net>
References: <200002021631.RAA12248@rs5.thch.uni-bonn.de> <3A09CB1E.12AD0F7B@mail.chem.tamu.edu>
Subject: Re: CCL:change basis set in G98
Date: Wed, 8 Nov 2000 17:28:09 -0800
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Hi!

This will work for Hartree-Fock SCF wave functions, I do not know about DFT
SCF wave functions.  A Hartree-Fock SCF wave function converged for a
particular basis set(s) stored in a checkpoint file can be used as a guess
for a future Hartree-Fock SCF convergence with a different basis set(s) on
the same molecule.  This is not the case for CIS (configuration
interaction).

Respectfully,
Phillip Matz

----- Original Message -----
From: "Huajun Fan" <fan@mail.chem.tamu.edu>
Cc: "Computational Chemistry List" <chemistry@server.ccl.net>
Sent: Wednesday, November 08, 2000 1:52 PM
Subject: CCL:change basis set in G98


> Hi everybody
>
> Can I use "guess=read" in route when changing basis set for an
> atom from one basis set to another? Will that cause any trouble
> when G98 read the wavefunction to the current geometry?  For
> example:
>
> ---first input---
> %Chk=first.chk
> %Mem=256MB
> %nproc=2
> # b3lyp/gen opt
>
> 0 1
> A 0. 0. 0.
> B 0. 1. 0.
> C 0. 0. 1.
>
> A 0
> 3-21G
> ****
> B 0
> 3-21G
> ****
> C 0
> 3-21G
> ****
>
>
> ---second input---
> %Chk=first.chk
> %Mem=256MB
> %nproc=2
> # b3lyp/gen opt guess=read geom=checkpoint
>
> 0 1
>
> A 0
> 3-21G
> ****
> B 0
> 6-311G**
> ****
> C 0
> 3-21G
> ****
>
> Since 3-21G is different than 6-311G**, will G98 read the
> wavefunction right? How guess=read was handled by G98? Can I do
> the same thing if I used 6-311G** for B atom first, then in the
> second calc. using 3-21G?
>
> Many thanks.
>
> huajun
>
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