From chemistry-request@server.ccl.net  Mon Dec 18 03:41:02 2000
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From: Thomas.Fox@bc.boehringer-ingelheim.com
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Subject: plot program
Date: Mon, 18 Dec 2000 09:40:34 +0100
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Hi,

does anybody know a program (preferentially on UNIX) which can do the
following:
take a series of quadruples (x,y,z,w), then plot x,y in a conventional 2D
dot plot, color the
dots according to z, and label the points with the contents of w. x,y,z
would be reals or integers,
w could be a number or a string. 

Thanks a lot,
Th.

Dr. Thomas Fox
Dept. Chemical Reseach / Structural Research
J51-00-01
Boehringer Ingelheim Pharma KG
88397 Biberach/Germany
Thomas.Fox@bc.boehringer-ingelheim.com


From chemistry-request@server.ccl.net  Mon Dec 18 05:37:54 2000
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Date: Mon, 18 Dec 2000 02:37:36 -0800 (PST)
From: Greg Lakatos <greg@fjohn.Stanford.EDU>
To: Ben Webb <ben@bellatrix.pcl.ox.ac.uk>
cc: chemistry@ccl.net
Subject: Re: CCL:CHARMm and MPICH
In-Reply-To: <Pine.LNX.4.21.0012171405010.8726-100000@bellatrix.pcl.ox.ac.uk>
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Thank you for the help.  Using:

./install.com gnu large M mpich

Seems to work however I get the error:

Enter the absolute path to the mpi include files (mpi.h, etc.)
/usr/local/mpich-1.2.1/include 
Enter the absolute path to the mpi lib files (e.g., libmpi.a(so)) >>
/usr/local/mpich-1.2.1/lib
ln: No match.                  

Compilation then proceeds normally and produces a CHARMM
executable.  However when I try to run this executable with:

mpirun -np 4 ./charmm < min.inp > min.out

CHARMM returns the error:

 Processing passed argument "-p4pg"
 Processing passed argument "-p4wd"
 RDTITL> No title read.
      ***** LEVEL 1 WARNING FROM <RDTITL> *****
      ***** Title expected.
      ******************************************
      BOMLEV ( 0) IS NOT REACHED. WRNLEV IS 5
 
An identical error is produced with the command line:

/ptemp/charmm -p4pg hosts -p4wd /ptemp < min.inp > min.out

(Thanks to Tru Huynh for his very helpful web page)

I have tried variations of these command lines involving combinations of
full and relative paths without any success. However with the command
line:

charmm < min.inp > min.out

CHARMM runs correctly (Albeit only on a single processor).  Do the CHARMM
command files need to be modified when running in parallel?

Thanks again for the help.

- Greg




From chemistry-request@server.ccl.net  Mon Dec 18 08:04:57 2000
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Date: Mon, 18 Dec 2000 14:04:45 +0100
From: Jacco van de Streek <jaccos@sci.kun.nl>
Organization: Dept. of Solid State Chem. 
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To: "chemistry@ccl.net" <chemistry@ccl.net>
CC: andreas.klamt@cosmologic.de
Subject: Re: CCL:Visualization of COSMO polarization charge densities and logP
References: <3A39DD61.1114EE7@cosmologic.de>
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Dr. Andreas Klamt wrote:
> As I pointed out in my COSMO-RS papers (for references see
> http://www.cosmologic.de) the polarization charge density sigma of a
> molecule embedded in a conductor is a very good, local descriptor for
> molecular interactions in solution. Indeed it is an even
> better descriptor than electrostatic potential (ESP), because ESP is rather
> longe-ranging while interactions are more local.
> As an example consider a surfactant with a positively charged head group.
> ESP shows a positive sign on the entire alkane chain of the surfactant,
> although this alkane chain behaves like a normal alkane chain.

Dear Dr Klamt,

I myself take an interest in the electrostatic properties of n-alkyl
fragments and find your concrete example very interesting.

Even though I'm interested in modelling crystal structures rather than
solutions, my interpretation of my own results on n-decylammonium seems
to contradict your statement, and I'd be interested in your comments.

When calculating the ESP derived charges of n-decylammonium using the
ChelpG option in Gaussian94 on a geometry-optimised molecule, SCF/HF
6-31G**, constraining the dipole moment of the point charges to its
quantum-mechanical value, my results are as follows (see the attached
Decylammonium.gif file):

- The ammonium group and the first methylene unit attached to it carry a
total charge of +0.9e.
- The remaining +0.1e is shared by the remaining 9 methylene units.

In my opinion, this seems reasonable for an n-alkyl chain. 

Where do our interpretations differ?

> Best regards
> 
> Jacco van de Streek
-- 
Jacco van de Streek (mailto:jaccos@sci.kun.nl)
Dept. of Solid State Chemistry
University of Nijmegen
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cssvxzxzzTfnvHPPPwc9dNFHJ710009HPXVPAwIAOw==
--------------F8EECDD3F2B6E208FB3E0EC6--



From chemistry-request@server.ccl.net  Mon Dec 18 08:12:47 2000
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From: "Juan Alexander Padron Garcia" <padrongj@cqf.co.cu>
To: <rasmol@lists.umass.edu>, "CCL" <chemistry@ccl.net>
Subject: Summary of Help with Homology SWISS-MODEL
Date: Mon, 18 Dec 2000 08:12:20 -0600
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Dear All:

First I would like to thanks to all the people who reply to my question. =
All the comments has been extremely usefull. Thanks again, Merry =
Chrismas and Happy New Millenium.

Best Regards,
Juan Alexander Padron
Molecular Modeling Laboratories
Pharmaceutical Chemistry Center
La Havana, Cuba

SUMARY

Question:
I have obtain a homology model of a protein of unknown structure using =
SWISS-MODEL, but I would like to validate the method in order to see if =
it works OK on this type of protein family. I think that the best way =
will be modeling a known structure of the family and finding the rmsd of =
the model with the real one, but I will need to tell to the program to =
ignore that PDB file from the RCSB. Is there a way to do that? Is there =
any program that could do it?=20

Answers
>From Gennady Poda:
check this out: =
http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html
>From Gales Rhodes
Use Deep View (SwissPdbViewer) for your homology modeling, and you will =
be
able to choose your templates rather than letting SwissModel choose them
for you.

For help with this, see

http://www.usm.maine.edu/spdbv/text/modeling.htm

If you are new to Deep View, see

http://www.usm.maine.edu/~rhodes/SPVTut/index.html

>From Don Gregory
Structural homology modeling has been around for quite some time,
and is regarded by many in the field, as a reliable method for
generating starting models.
Generally, the 'lower-limit' people have found, by experience, is
that of having 30% identity in the area of interest, whether it is
the whole protein, a domain, or an active site.  Of course,
evolutionary pressures tend to make the identity quite a bit higher
in active sites.
Several excellent papers on the techniques can be found on the
web-site of Professor Andrej Sali, Rockefeller University.  He
has created an automated homology program, called Modeler.
http://guitar.rockefeller.edu/publications/ref/ref.html

Another thing I could suggest, would be to find a *family* of
similar structures.  Use one as the template, and build by
homology, another family memeber who's structure is known,
and then see how 'acceptable' that is to you.
I might suggest using something like Profiles-3D to test the
validity of the build model as well.  This is a program developed
by Professor David Eisenburg at UCLA, and is quite well
respected in 'testing' a build model with respect to its likelihood
of being a reasonable structure.  You can find more info on this
at:
http://www.doe-mbi.ucla.edu/people/fischer/BENCH/benchmark1.html



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Content-Transfer-Encoding: quoted-printable

<!DOCTYPE HTML PUBLIC "-//W3C//DTD W3 HTML//EN">
<HTML>
<HEAD>

<META content=3Dtext/html;charset=3Diso-8859-1 =
http-equiv=3DContent-Type>
<META content=3D'"MSHTML 4.72.3110.7"' name=3DGENERATOR>
</HEAD>
<BODY bgColor=3D#ffffff>
<DIV><FONT color=3D#000000 size=3D2>Dear All:</FONT></DIV>
<DIV><FONT color=3D#000000 size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT color=3D#000000 size=3D2>First I would like to thanks to all =
the people=20
who reply to my question. All the comments has been extremely usefull. =
Thanks=20
again, Merry Chrismas and Happy New Millenium.</FONT></DIV>
<DIV><FONT color=3D#000000 size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT color=3D#000000 size=3D2>Best Regards,</FONT></DIV>
<DIV><FONT color=3D#000000 size=3D2>Juan Alexander Padron</FONT></DIV>
<DIV><FONT color=3D#000000 size=3D2>Molecular Modeling =
Laboratories</FONT></DIV>
<DIV><FONT color=3D#000000 size=3D2>Pharmaceutical Chemistry =
Center</FONT></DIV>
<DIV><FONT color=3D#000000 size=3D2>La Havana, Cuba</FONT></DIV>
<DIV><FONT color=3D#000000 size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT color=3D#000000 size=3D2>SUMARY</FONT></DIV>
<DIV><FONT color=3D#000000 size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT color=3D#000000 size=3D2>Question:</FONT></DIV>
<DIV><FONT color=3D#000000 size=3D2></FONT><FONT color=3D#000000 =
size=3D2>I have obtain=20
a homology model of a protein of unknown structure using SWISS-MODEL, =
but I=20
would like to validate the method in order to see if it works OK on this =
type of=20
protein family. I think that the best way will be modeling a known =
structure of=20
the family and finding the rmsd of the model with the real one, but I =
will need=20
to tell to the program to ignore that PDB file from the RCSB. Is there a =
way to=20
do that? Is there any program that could do it? </FONT></DIV>
<DIV><FONT color=3D#000000 size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT color=3D#000000 size=3D2>Answers</FONT></DIV>
<DIV><FONT color=3D#000000 size=3D2></FONT><FONT size=3D2>From <SPAN=20
class=3D098394514-14122000><FONT color=3D#000000 face=3DArial =
size=3D2>Gennady=20
Poda:</FONT></SPAN></FONT></DIV>
<DIV><FONT size=3D2><SPAN class=3D098394514-14122000><FONT =
color=3D#000000 face=3DArial=20
size=3D2></FONT></SPAN></FONT>
<DIV><FONT face=3DArial size=3D2><SPAN class=3D098394514-14122000><FONT=20
color=3D#000000>check this out: </FONT></SPAN></FONT><FONT =
face=3DTahoma><A=20
href=3D"http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html"><FONT=
=20
color=3D#000000 face=3D""=20
size=3D2>http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html</FONT=
></A></FONT></DIV>
<BLOCKQUOTE style=3D"MARGIN-RIGHT: 0px"></BLOCKQUOTE></DIV>
<DIV><FONT color=3D#000000 size=3D2>From Gales Rhodes</FONT></DIV>
<DIV><FONT color=3D#000000 size=3D2>Use Deep View (SwissPdbViewer) for =
your homology=20
modeling, and you will be<BR>able to choose your templates rather than =
letting=20
SwissModel choose them<BR>for you.<BR><BR>For help with this, =
see<BR><BR><A=20
href=3D"http://www.usm.maine.edu/spdbv/text/modeling.htm">http://www.usm.=
maine.edu/spdbv/text/modeling.htm</A><BR><BR>If=20
you are new to Deep View, see<BR><BR><A=20
href=3D"http://www.usm.maine.edu/~rhodes/SPVTut/index.html">http://www.us=
m.maine.edu/~rhodes/SPVTut/index.html</A></FONT></DIV>
<DIV><FONT color=3D#000000 size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT color=3D#000000 size=3D2>From Don Gregory</FONT></DIV>
<DIV><FONT color=3D#000000 size=3D2>Structural homology modeling has =
been around for=20
quite some time,<BR>and is regarded by many in the field, as a reliable =
method=20
for<BR>generating starting models.<BR>Generally, the 'lower-limit' =
people have=20
found, by experience, is<BR>that of having 30% identity in the area of =
interest,=20
whether it is<BR>the whole protein, a domain, or an active site.&nbsp; =
Of=20
course,<BR>evolutionary pressures tend to make the identity quite a bit=20
higher<BR>in active sites.<BR>Several excellent papers on the techniques =
can be=20
found on the<BR>web-site of Professor Andrej Sali, Rockefeller =
University.&nbsp;=20
He<BR>has created an automated homology program, called Modeler.<BR><A=20
href=3D"http://guitar.rockefeller.edu/publications/ref/ref.html">http://g=
uitar.rockefeller.edu/publications/ref/ref.html</A><BR><BR>Another=20
thing I could suggest, would be to find a *family* of<BR>similar=20
structures.&nbsp; Use one as the template, and build by<BR>homology, =
another=20
family memeber who's structure is known,<BR>and then see how =
'acceptable' that=20
is to you.<BR>I might suggest using something like Profiles-3D to test=20
the<BR>validity of the build model as well.&nbsp; This is a program=20
developed<BR>by Professor David Eisenburg at UCLA, and is quite=20
well<BR>respected in 'testing' a build model with respect to its=20
likelihood<BR>of being a reasonable structure.&nbsp; You can find more =
info on=20
this<BR>at:<BR><A=20
href=3D"http://www.doe-mbi.ucla.edu/people/fischer/BENCH/benchmark1.html"=
>http://www.doe-mbi.ucla.edu/people/fischer/BENCH/benchmark1.html</A></FO=
NT></DIV>
<DIV><FONT color=3D#000000 size=3D2></FONT>&nbsp;</DIV>
<DIV>&nbsp;</DIV></BODY></HTML>

------=_NextPart_000_0076_01C068CA.3EB67000--



From chemistry-request@server.ccl.net  Mon Dec 18 08:46:32 2000
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Date: Mon, 18 Dec 2000 21:48:51 +0800
From: Ji Hai-tao <caddk@online.sh.cn>
To: "chemistry@ccl.net" <chemistry@ccl.net>
Subject: IR software
Organization: School of pharmacy, second military medical university
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Dear sir,
I need to have a free IR software to read a IR spectrum file.
However, I didn't have one at hand.Does anyone can tell me 
where I can get a free software?

Song Yunlong,PhD



From chemistry-request@server.ccl.net  Mon Dec 18 09:58:52 2000
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Date: Mon, 18 Dec 2000 15:58:36 +0100
From: Frank Oellien <Frank.Oellien@chemie.uni-erlangen.de>
Organization: Computer-Chemie-Centrum - http://www2.ccc.uni-erlangen.de/ChemVis/
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Subject: Electrostatic Potential with Gaussian
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Hello,

how can I obtain a CUBE file with electrostatic potential information?
I have already received a CUBE file with density information with the
following input:

$rungaus
#N STO-3G OPT FormCheck=ALL CUBE=Density Prop=Grid

ethan

0 1
C 0.765 0.0 0.0
C -0.765 0.0 0.0
H 1.1283 -0.0097 1.0276
H 1.1283 -0.8851 -0.5222
H 1.1283 0.8948 -0.5054
H -1.1283 -0.8948 0.5054
H -1.1283 0.8851 0.5222
H -1.1283 0.0097 -1.0276

c2h6_dens.cube

However, the CUBE file generation for EPOT will not work with this
input:

$rungaus
#N STO-3G OPT CUBE=Potential Prop=Potential

ethan

0 1
C 0.765 0.0 0.0
C -0.765 0.0 0.0
H 1.1283 -0.0097 1.0276
H 1.1283 -0.8851 -0.5222
H 1.1283 0.8948 -0.5054
H -1.1283 -0.8948 0.5054
H -1.1283 0.8851 0.5222
H -1.1283 0.0097 -1.0276

c2h6_epot.cube

I use Gaussian 94. The log files show that Gaussian terminates normal.

With regards

Frank Oellien


--
Computer-Chemistry-Center and Institute of Organic Chemistry
University of Erlangen-Nuernberg
Naegelsbachstrasse 25, D-91052 Erlangen (Germany)
Tel (+49)-(0)9131-85-26579  Fax (+49)-(0)9131-85-26566
email: Frank.Oellien@chemie.uni-erlangen.de
WWW  : http://www2.ccc.uni-erlangen.de/oellien/
       http://www2.ccc.uni-erlangen.de/ChemVis/




From chemistry-request@server.ccl.net  Mon Dec 18 10:30:42 2000
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Message-ID: <3A3E2D92.38BE0297@cosmologic.de>
Date: Mon, 18 Dec 2000 16:30:26 +0100
From: "Dr. Andreas Klamt" <andreas.klamt@cosmologic.de>
Organization: COSMOlogic GmbH&CoKG
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To: Jacco van de Streek <jaccos@sci.kun.nl>,
        "chemistry@ccl.net" <chemistry@ccl.net>
Subject: Re: CCL:Visualization of COSMO polarization charge densities and logP
References: <3A39DD61.1114EE7@cosmologic.de> <3A3E0B6D.826D798@sci.kun.nl>
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Dear Dr. de Streek,

I think we do not differ at all. You are talking about ESP fitted charge,
I am talking about ESP visualized on the surface. Even
though the ESP on such a chain is rather long-ranging,
i.e. the potential will have the positive signe of the head-group quite
far along the chain, the backfitted point-charges will be rather
localized. My point is, that using the ESP itself as a
descriptor of polarity on the molecular surface would be misleading.

Best regards

Andreas


--------------------------------------------------------------------------------
Dr. Andreas Klamt
COSMOlogic GmbH&CoKG
Burscheider Str. 515
51381 Leverkusen, Germany

Tel.: 49-2171-73168-1  Fax: ...-9
e-mail: andreas.klamt@cosmologic.de
web:    www.cosmologic.de
--------------------------------------------------------------------------------
COSMOlogic
        Your Competent Partner for
        Computational Chemistry and Fluid Thermodynamics
--------------------------------------------------------------------------------


From chemistry-request@server.ccl.net  Mon Dec 18 11:23:11 2000
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From: "Gavin Shear" <gavin@acdlabs.com>
To: "Ji Hai-tao" <caddk@online.sh.cn>, <chemistry@ccl.net>
Subject: RE: IR software
Date: Mon, 18 Dec 2000 11:28:33 -0500
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Advanced Chemistry Development offers 
free SpecViewer 4.5, which, when installed
with free ChemSketch 4.5 allows the viewing,
processing, and report editing for MS, NMR,
UVIR/Raman Spectra.

Input formats available are JCAMP, ASCII (*.txt),
Galactic (*.spc) and ACD (*.esp) formats.

Free download is available at www.acdlabs.com/download

The software is licensed for home or educational use 
only. If you are an industrial user, you must obtain a 
commercial license.

For more information about our commercial IR software,
please visit:
http://www.acdlabs.com/products/spec_lab/exp_spectra/uv_ir/

Many thanks,
Gavin



> -----Original Message-----
> From: Computational Chemistry List 
> [mailto:chemistry-request@ccl.net]On Behalf Of Ji Hai-tao
> Sent: 18 December 2000 08:49
> To: chemistry@ccl.net
> Subject: CCL:IR software
> 
> 
> Dear sir,
> I need to have a free IR software to read a IR spectrum file.
> However, I didn't have one at hand.Does anyone can tell me 
> where I can get a free software?
> 
> Song Yunlong,PhD
> 
> 
> 
> -= This is automatically added to each message by mailing script =-
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From chemistry-request@server.ccl.net  Mon Dec 18 12:34:40 2000
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To: "Frank Oellien" <Frank.Oellien@chemie.uni-erlangen.de>,
        <chemistry@ccl.net>
References: <3A3E261B.89D02449@chemie.uni-erlangen.de>
Subject: Re: CCL:Electrostatic Potential with Gaussian
Date: Mon, 18 Dec 2000 09:34:20 -0800
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Hello Dr. Oellien,

I think the reason your job is not completeing is because it should be a
compound job.  The OPT keyword will generate multiple SCFs associated with
each step in the geometry optimization, and Gaussian will try and save a
cube file for each.  Splitting the OPT job and the CUBE job into two files
seemed to do the trick (I have appended the compound job to the end of this
email).  I hope this works!

Respectfully,
Phillip Matz

matz@wsunix.wsu.edu


%chk=test.chk
#N STO-3G OPT

ethan

0 1
C 0.765 0.0 0.0
C -0.765 0.0 0.0
H 1.1283 -0.0097 1.0276
H 1.1283 -0.8851 -0.5222
H 1.1283 0.8948 -0.5054
H -1.1283 -0.8948 0.5054
H -1.1283 0.8851 0.5222
H -1.1283 0.0097 -1.0276

--LINK1--
%chk=test.chk
#N STO-3G CUBE=Potential Prop=Potential geom=checkpoint

ethan

0 1

c2h6_epot.cube


----- Original Message -----
From: "Frank Oellien" <Frank.Oellien@chemie.uni-erlangen.de>
To: <chemistry@ccl.net>
Sent: Monday, December 18, 2000 6:58 AM
Subject: CCL:Electrostatic Potential with Gaussian


> Hello,
>
> how can I obtain a CUBE file with electrostatic potential information?
> I have already received a CUBE file with density information with the
> following input:
>
> $rungaus
> #N STO-3G OPT FormCheck=ALL CUBE=Density Prop=Grid
>
> ethan
>
> 0 1
> C 0.765 0.0 0.0
> C -0.765 0.0 0.0
> H 1.1283 -0.0097 1.0276
> H 1.1283 -0.8851 -0.5222
> H 1.1283 0.8948 -0.5054
> H -1.1283 -0.8948 0.5054
> H -1.1283 0.8851 0.5222
> H -1.1283 0.0097 -1.0276
>
> c2h6_dens.cube
>
> However, the CUBE file generation for EPOT will not work with this
> input:
>
> $rungaus
> #N STO-3G OPT CUBE=Potential Prop=Potential
>
> ethan
>
> 0 1
> C 0.765 0.0 0.0
> C -0.765 0.0 0.0
> H 1.1283 -0.0097 1.0276
> H 1.1283 -0.8851 -0.5222
> H 1.1283 0.8948 -0.5054
> H -1.1283 -0.8948 0.5054
> H -1.1283 0.8851 0.5222
> H -1.1283 0.0097 -1.0276
>
> c2h6_epot.cube
>
> I use Gaussian 94. The log files show that Gaussian terminates normal.
>
> With regards
>
> Frank Oellien
>
>
> --
> Computer-Chemistry-Center and Institute of Organic Chemistry
> University of Erlangen-Nuernberg
> Naegelsbachstrasse 25, D-91052 Erlangen (Germany)
> Tel (+49)-(0)9131-85-26579  Fax (+49)-(0)9131-85-26566
> email: Frank.Oellien@chemie.uni-erlangen.de
> WWW  : http://www2.ccc.uni-erlangen.de/oellien/
>        http://www2.ccc.uni-erlangen.de/ChemVis/
>
>
>
>
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From chemistry-request@server.ccl.net  Mon Dec 18 18:06:16 2000
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	Mon, 18 Dec 2000 15:48:40 -0600
Date: Mon, 18 Dec 2000 15:48:40 -0600 (CST)
From: Ali N Rashid <rrashid@unlserve.unl.edu>
To: Zhenyu Lu <zl2@duke.edu>
cc: chemistry@ccl.net
Subject: Re: CCL:IRC reaction path  geometres
In-Reply-To: <002601c068a5$e87be4a0$8da90398@chem.duke.edu>
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Try writing a routine that uses as input the gausian output file. Then
specify that the program write individual files with the coordinates of
each point in the reaction. Use newzmat to change the coordinates to pdb.

There is a program called Molden that allows to make movies of IRC
calculations. This might help as well.

Good luck.

Ali


On Sun, 17 Dec 2000, Zhenyu Lu wrote:

> Hi, I was using Gaussian 98, ran reaction path calculations.
> I used keyword IRC, doing forward and backword reactons. 
> In the gaussian output file, you will  see geometres and energes
> of each point are listed as a table. 
> My question is:
> How can I convert one Gaussian output file  to PDB files or XYZ
> files,  each PDB/XYZ  file for just one point along the reaction path?
> 
> I know Gaussian provides some unitily, like newzmat, which can  
> make a convertion between different file  types, but I don't know how to use it
> to solve my question above.
> 
> Thanks in advance.
> Zhenyu Lu
> Dept of Chem, Duke Univ.
> 
> 
>   
>