From owner-chemistry@ccl.net Thu Jul 24 00:25:00 2008
From: "izwan zainurul zainurulizwan80|-|yahoo.com" <owner-chemistry%a%server.ccl.net>
To: CCL
Subject: CCL: simulation period
Message-Id: <-37406-080721001147-14976-zfr6i50Ech0EWm5iQn4bbA%a%server.ccl.net>
X-Original-From: izwan zainurul <zainurulizwan80::yahoo.com>
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Sent to CCL by: izwan zainurul [zainurulizwan80 _ yahoo.com]

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Hai all,
=A0
I had done molecular dynamics to find global minimum for cyclodextrin compl=
ex. I used Chem3D program to run my molecular dynamics. How do I know I run=
 simulation period adequately? Thanks you.
=A0
- Izwan=0A=0A=0A      
--0-857659351-1216609895=:16029
Content-Type: text/html; charset=us-ascii

<table cellspacing='0' cellpadding='0' border='0' ><tr><td valign='top' style='font: inherit;'><P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT face="Times New Roman" size=3>Hai all,</FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" /><o:p><FONT face="Times New Roman" size=3>&nbsp;</FONT></o:p></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT face="Times New Roman" size=3>I had done molecular dynamics to find global minimum for cyclodextrin complex. I used Chem3D program to run my molecular dynamics. How do I know I run simulation period adequately? Thanks you.</FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><o:p><FONT face="Times New Roman" size=3>&nbsp;</FONT></o:p></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT face="Times New Roman" size=3>- Izwan</FONT></P></td></tr></table><br>

      
--0-857659351-1216609895=:16029--


From owner-chemistry@ccl.net Thu Jul 24 01:02:00 2008
From: "izwan zainurul zainurulizwan80-#-yahoo.com" <owner-chemistry-,-server.ccl.net>
To: CCL
Subject: CCL: simulation period
Message-Id: <-37407-080720234547-6196-2RDTRT2msSiDENvGEGjzDA-,-server.ccl.net>
X-Original-From: izwan zainurul <zainurulizwan80/./yahoo.com>
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Date: Sun, 20 Jul 2008 20:18:56 -0700 (PDT)
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Sent to CCL by: izwan zainurul [zainurulizwan80||yahoo.com]

--0-923787823-1216610336=:67908
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Hai all,
=A0
I had done molecular dynamics to find global minimum for cyclodextrin compl=
ex. I used Chem3D program to run my molecular dynamics. How do I know I run=
 simulation period adequately? Thanks you.
=A0
- Izwan=0A=0A=0A      
--0-923787823-1216610336=:67908
Content-Type: text/html; charset=us-ascii

<table cellspacing='0' cellpadding='0' border='0' ><tr><td valign='top' style='font: inherit;'><P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT face="Times New Roman" size=3>Hai all,</FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" /><o:p><FONT face="Times New Roman" size=3>&nbsp;</FONT></o:p></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT face="Times New Roman" size=3>I had done molecular dynamics to find global minimum for cyclodextrin complex. I used Chem3D program to run my molecular dynamics. How do I know I run simulation period adequately? Thanks you.</FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><o:p><FONT face="Times New Roman" size=3>&nbsp;</FONT></o:p></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT face="Times New Roman" size=3>- Izwan</FONT></P></td></tr></table><br>

      
--0-923787823-1216610336=:67908--


From owner-chemistry@ccl.net Thu Jul 24 04:00:00 2008
From: "Pascal Boulet pascal.boulet..univ-provence.fr" <owner-chemistry*server.ccl.net>
To: CCL
Subject: CCL: simulation period
Message-Id: <-37408-080724035459-29527-mJ7d7p2hgKOU2TRtdSQEOg*server.ccl.net>
X-Original-From: Pascal Boulet <pascal.boulet[a]univ-provence.fr>
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Date: Thu, 24 Jul 2008 09:23:08 +0200
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Sent to CCL by: Pascal Boulet [pascal.boulet%univ-provence.fr]
This is a multi-part message in MIME format.
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Hi Izwan,

First, you are never sure that you found the _global_ minimum, 
especially for very large molecules such biological ones. At least you 
can check whether you got a _local _minimum or a _local_ maximum.

The best way to see if your system is equilibrated is to glance at the 
energy vs time step. If the energy is fluctuating around a constant 
value over the simulation, then the system is equilibrated. You can 
check this by performing block averages of the energy.

Hope this help,
Pascal




izwan zainurul zainurulizwan80|-|yahoo.com wrote:
>
> Hai all,
>
>  
>
> I had done molecular dynamics to find global minimum for cyclodextrin 
> complex. I used Chem3D program to run my molecular dynamics. How do I 
> know I run simulation period adequately? Thanks you.
>
>  
>
> - Izwan
>
>

-- 
Dr. Pascal Boulet, Computational Chemist
University of Provence
Laboratoire Chimie Provence, UMR6264
Centre Saint-Jerome, case MADIREL
F-13397 MARSEILLE Cedex 20, France
Tel. +33 (0) 491 63 71 17 Fax. +33 (0) 491 63 71 11
courriel: pascal.boulet#%#univ-provence.fr
http://www.lc-provence.fr
http://allos.up.univ-mrs.fr/boulet


--------------070508090100000606000203
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  <meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type">
  <title></title>
</head>
<body bgcolor="#ffffff" text="#000000">
Hi Izwan,<br>
<br>
First, you are never sure that you found the <u>global</u> minimum,
especially for very large molecules such biological ones. At least you
can check whether you got a <u>local </u>minimum or a <u>local</u>
maximum.<br>
<br>
The best way to see if your system is equilibrated is to glance at the
energy vs time step. If the energy is fluctuating around a constant
value over the simulation, then the system is equilibrated. You can
check this by performing block averages of the energy.<br>
<br>
Hope this help,<br>
Pascal<br>
<br>
<br>
<br>
<br>
izwan zainurul zainurulizwan80|-|yahoo.com wrote:
<blockquote
 cite="mid:-id%234y6-37406-080721001147-14976-K0GQzauotTEM1qovQPa80A#%#server.ccl.net"
 type="cite">
  <table border="0" cellpadding="0" cellspacing="0">
    <tbody>
      <tr>
        <td
 style="font-family: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; font-size: inherit; line-height: inherit; font-size-adjust: inherit; font-stretch: inherit;"
 valign="top">
        <p class="MsoNormal" style="margin: 0in 0in 0pt;"><font
 face="Times New Roman" size="3">Hai all,</font></p>
        <p class="MsoNormal" style="margin: 0in 0in 0pt;"><o:p><font
 face="Times New Roman" size="3">&nbsp;</font></o:p></p>
        <p class="MsoNormal" style="margin: 0in 0in 0pt;"><font
 face="Times New Roman" size="3">I had done molecular dynamics to find
global minimum for cyclodextrin complex. I used Chem3D program to run
my molecular dynamics. How do I know I run simulation period
adequately? Thanks you.</font></p>
        <p class="MsoNormal" style="margin: 0in 0in 0pt;"><o:p><font
 face="Times New Roman" size="3">&nbsp;</font></o:p></p>
        <p class="MsoNormal" style="margin: 0in 0in 0pt;"><font
 face="Times New Roman" size="3">- Izwan</font></p>
        </td>
      </tr>
    </tbody>
  </table>
  <br>
</blockquote>
<br>
<pre class="moz-signature" cols="72">-- 
Dr. Pascal Boulet, Computational Chemist
University of Provence
Laboratoire Chimie Provence, UMR6264
Centre Saint-Jerome, case MADIREL
F-13397 MARSEILLE Cedex 20, France
Tel. +33 (0) 491 63 71 17 Fax. +33 (0) 491 63 71 11
courriel: <a class="moz-txt-link-abbreviated" href="mailto:pascal.boulet#%#univ-provence.fr">pascal.boulet#%#univ-provence.fr</a>
<a class="moz-txt-link-freetext" href="http://www.lc-provence.fr">http://www.lc-provence.fr</a>
<a class="moz-txt-link-freetext" href="http://allos.up.univ-mrs.fr/boulet">http://allos.up.univ-mrs.fr/boulet</a>
</pre>
</body>
</html>

--------------070508090100000606000203--


From owner-chemistry@ccl.net Thu Jul 24 09:43:01 2008
From: "=?GB2312?B?wbrLrA==?= lsveracool^^gmail.com" <owner-chemistry _ server.ccl.net>
To: CCL
Subject: CCL:G: a question about solvent computation
Message-Id: <-37409-080723112059-15552-AMnHvqgEBU7lD0WFLWn85w _ server.ccl.net>
X-Original-From: "=?GB2312?B?wbrLrA==?=" <lsveracool===gmail.com>
Content-Type: multipart/alternative; 
	boundary="----=_Part_71912_6406180.1216823132264"
Date: Wed, 23 Jul 2008 22:25:32 +0800
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Sent to CCL by: "=?GB2312?B?wbrLrA==?=" [lsveracool===gmail.com]

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the head file is :
#p hf/6-311++g** scf=tight scrf(pcm,read,solvent=water)

the error termination is :
Annihilation of the first spin contaminant:
 S**2 before annihilation     0.8506,   after     0.7572
 Convergence failure -- run terminated.
 Error termination via Lnk1e in /home/user/ustcguo/g03/l502.exe at Wed Jul
23 22:02:34 2008.
 Job cpu time:  0 days  0 hours 31 minutes 45.5 seconds.
 File lengths (MBytes):  RWF=     82 Int=      0 D2E=      0 Chk=      2
Scr=      1

DeltaG (solv)                            (kcal/mol) =     -64.82
the result comes out, but I wonder whether it is correct. because I 've
calculated a file which gave two different DeltaGs on two mechines.

thanks for the help!

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<div dir="ltr"><div>the head file is :</div>
<div>#p hf/6-311++g** scf=tight scrf(pcm,read,solvent=water)</div>
<div>&nbsp;</div>
<div>the error termination is :</div>
<div>Annihilation of the first spin contaminant:<br>&nbsp;S**2 before annihilation&nbsp;&nbsp;&nbsp;&nbsp; 0.8506,&nbsp;&nbsp; after&nbsp;&nbsp;&nbsp;&nbsp; 0.7572<br>&nbsp;Convergence failure -- run terminated.<br>&nbsp;Error termination via Lnk1e in /home/user/ustcguo/g03/l502.exe at Wed Jul 23 22:02:34 2008.<br>
&nbsp;Job cpu time:&nbsp; 0 days&nbsp; 0 hours 31 minutes 45.5 seconds.<br>&nbsp;File lengths (MBytes):&nbsp; RWF=&nbsp;&nbsp;&nbsp;&nbsp; 82 Int=&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0 D2E=&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0 Chk=&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2 Scr=&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1</div>
<div>&nbsp;</div>
<div>DeltaG (solv)&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; (kcal/mol) =&nbsp;&nbsp;&nbsp;&nbsp; -64.82</div>
<div>the result comes out, but&nbsp;I wonder&nbsp;whether it is correct. because I &#39;ve calculated a file which gave two different DeltaGs on two mechines.</div>
<div>&nbsp;</div>
<div>thanks for the help!</div></div>

------=_Part_71912_6406180.1216823132264--


From owner-chemistry@ccl.net Thu Jul 24 13:16:00 2008
From: "=?ISO-8859-1?Q?Ren=E9_Kanters?= rkanters(_)richmond.edu" <owner-chemistry#server.ccl.net>
To: CCL
Subject: CCL:G: Optimization with imaginary frequency
Message-Id: <-37410-080724123206-1131-Yz55mH/NEoc1dA2geEAyXg#server.ccl.net>
X-Original-From: =?ISO-8859-1?Q?Ren=E9_Kanters?= <rkanters=richmond.edu>
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Sent to CCL by: =?ISO-8859-1?Q?Ren=E9_Kanters?= [rkanters++richmond.edu]
Hi Flavio,

I hacked together a little perl scrip that will look at the first set =20=

frequency information in a gaussian calculation and generate a new =20
set of xyz coordinates in which the structure is moved along a =20
vibrational coordinate for a certain amount (see the command line =20
arguments in the script below).

Note that it may be necessary, depending on the symmetry of the =20
saddlepoint you got to create a new input with going in the positive =20
and another one in the negative direction of the imaginary frequency =20
since you can't be sure which one will lead you to a lower minimum.

I hope this helps.

Ren=E9

PS it's not pretty (I am not a perl programmer), but it has worked =20
for me.

#! /usr/bin/perl
###############################################
# script to take a gaussian log file output and generate structure
# information (cartesian) for a new structure with a displacement
# along a frequency coordinate in the direction along the '-v' vibration
# for a displacement of '-d' times the vibrational vector
#
# command line arguments:
#
# -h        : prints help and quits.
# -d float  : displacement along vibrational mode default 0.1
# -v int    : vibration number to use default 1
# required : filename (only sees last one)
################################################

#
$test =3D 0;  # for debugging purposes (prints out extra stuff)

# set up the defaults
$vibration =3D 1;
$displacement =3D 0.1;
$file =3D "";

# 'constants' not using the 'use constant NAME =3D> value;' method.
$C_STRUCTURE =3D "Standard orientation:";
$C_ENDSTRUCTURE =3D "---------";
$C_FREQUENCY =3D "Frequencies --";

while ($#ARGV >=3D 0) {
   if ($ARGV[0] eq "-d")    { $displacement =3D $ARGV[1]; shift |-|ARGV; }
   elsif ($ARGV[0] eq "-v") { $vibration =3D $ARGV[1]; shift |-|ARGV; }
   elsif ($ARGV[0] eq "-h") { &usage(); exit;}
   else { $file =3D $ARGV[0];}
   shift |-|ARGV;
}

if ($file eq "") { &usage(); exit;}

open(IN,$file) || die "Could not open file '$file'.\n";

while (1) {
   # read until I get a structure (should happen first) or a frequency
   until ($_ =3D <IN>, $_ =3D~ /$C_STRUCTURE/ or $_ =3D~ /$C_FREQUENCY/ =
or =20
eof) { }
   if ($_ =3D~ /$C_STRUCTURE/) {  # READ THE STRUCTURE
     $nat =3D -1;   # reset the atom index counter : only need last =20
structure
     $at =3D ();    # clear out the arrays of atomnumber, x, y and z
     $x =3D ();
     $y =3D ();
     $z =3D ();
     skiplines(4); # position read line to first atom in the list
     while ($_ =3D <IN> and not $_ =3D~ /$C_ENDSTRUCTURE/ ) {
       |-|tokens =3D split(' ', $_);
       $nat++;
       $at[$nat] =3D $tokens[1];
       $xind =3D $#tokens - 2; # needed if the atomic type is missing =20=

(happens sometimes).
       $x[$nat] =3D $tokens[$xind];
       $y[$nat] =3D $tokens[$xind+1];
       $z[$nat] =3D $tokens[$xind+2];
     }
   } elsif ($_ =3D~ /$C_FREQUENCY/) { # READ THE FREQUENCY INFORMATION
     # since there are three vibrations per line, I can determine how
     # many of these I need to skip before I can read the frequency I =20=

need.
     $skipsize =3D 4 + ($nat+1) + 3;  # skip rest header, vibrations =20
and start header
     for ($i=3D0; $i<int($vibration/3); $i++) { skiplines($skipsize); }

     skiplines(4);
     $xind =3D 2 + (($vibration-1) % 3) * 3; # position in the tokens =20=

of vib vector
     if ($test eq 1) { print "vibration =3D $vibration, xind =3D =
$xind\n"; }
     for ($i=3D0;$i<=3D$nat;$i++) {
       $_ =3D <IN>;
       |-|tokens =3D split(' ',$_);
       if ($test eq 1 ) {
         print "input $_";
         print "($x[$i],$y[$i],$z[$i]) + $displacement x ($tokens=20
[$xind],$tokens[$xind+1],$tokens[$xind+2])\n";
       }
       printf "%4d  % .6f  % .6f  % .6f\n",$at[$i], $x[$i]+=20
$displacement*$tokens[$xind], $y[$i]+$displacement*$tokens[$xind+1], =20
$z[$i]+$displacement*$tokens[$xind+2];
     }
     exit; # AND WE ARE DONE!!!!
   } elsif (eof) { close IN; exit; }
}

##################################################
# skiplines : argument n: number of lines to skip
##################################################
sub skiplines {
   local $n, $i;
   $n =3D shift(|-|_);
   for ($i=3D0;$i<$n;$i++) { <IN> || die "skiplines encountered EOF."; }
}


##################################################
# usage prints a message about how to use sp2g03
##################################################
sub usage {
print <<ENDUSAGE;
Usage: nfreq [-h] [-d displacement] [-v vibrationnnumber] filename

-d : displacement step along vibrational mode default 0.1
-v : index of vibrational mode to follow default 1
-h : prints this help

Will create the structure '-d' along the '-v'th vibrational mode of =20
the stucture.
ENDUSAGE
}

On Jul 23, 2008, at 3:39 PM, flavio forti fforti.:.fortisrl.com.ar =20
wrote:

>
> Sent to CCL by: "flavio  forti" [fforti^_^fortisrl.com.ar]
> Hi everybody. I am trying to optimize a large set of histamine =20
> monocation  conformers in solution (PCM) with B3LYP/6-31G*. I had =20
> some which converged to a saddle point (1 imaginary frequency) but =20
> finally, after several reoptimizations with CalcFC they arrived to =20
> a minimum. But there is one still resisting. CalcAll would be to =20
> expensive, what do you suggest?
> thanks
> flavio
>
>
>
> -=3D This is automatically added to each message by the mailing =20
> script =3D-
> To recover the email address of the author of the message, please =20
> change> Conferences: http://server.ccl.net/chemistry/announcements/=20
> conferences/
>
> Search Messages: http://www.ccl.net/htdig  (login: ccl, Password: =20
> search)>
>


From owner-chemistry@ccl.net Thu Jul 24 15:01:00 2008
From: "Ol Ga eurisco1%x%pochta.ru" <owner-chemistry_._server.ccl.net>
To: CCL
Subject: CCL:G: a question about solvent computation
Message-Id: <-37411-080724145650-6765-i/kYX1HdDDEHy/gHqWB0Fw_._server.ccl.net>
X-Original-From: "Ol  Ga" <eurisco1#,#pochta.ru>
Date: Thu, 24 Jul 2008 14:56:46 -0400


Sent to CCL by: "Ol  Ga" [eurisco1],[pochta.ru]
Dear Isveracool,

your job running was aborted during a SCF- procedure and there is severe spin contamination.
So, I think that the correct route section should be 

#p uhf/6-311++g** scf=(vshift=100,xqc,tight,maxcycle=512) 
# scrf(pcm,read,solvent=water)


Sincerely,
Ol Ga


ps. if you get an error in SCF-procedure try to use DAMP and NDamp keywords in an appropriate way or change the basis set.



----- Original Message ----- 
> From:  lsveracool^^gmail.com 
To: Ga, Ol  
Sent: Wednesday, July 23, 2008 6:25 PM
Subject: CCL:G: a question about solvent computation


the head file is :
#p hf/6-311++g** scf=tight scrf(pcm,read,solvent=water)

the error termination is :
Annihilation of the first spin contaminant:
 S**2 before annihilation     0.8506,   after     0.7572
 Convergence failure -- run terminated.
 Error termination via Lnk1e in /home/user/ustcguo/g03/l502.exe at Wed Jul 23 22:02:34 2008.
 Job cpu time:  0 days  0 hours 31 minutes 45.5 seconds.
 File lengths (MBytes):  RWF=     82 Int=      0 D2E=      0 Chk=      2 Scr=      1

DeltaG (solv)                            (kcal/mol) =     -64.82
the result comes out, but I wonder whether it is correct. because I 've calculated a file which gave two different DeltaGs on two mechines.

thanks for the help!


From owner-chemistry@ccl.net Thu Jul 24 16:16:00 2008
From: "Sten Nilsson Lill stenil .. chem.gu.se" <owner-chemistry{}server.ccl.net>
To: CCL
Subject: CCL:G: Optimization with imaginary frequency
Message-Id: <-37412-080724154649-10318-mqr/KkTbtrh5iMS8c48klg{}server.ccl.net>
X-Original-From: "Sten Nilsson Lill" <stenil * chem.gu.se>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain;charset=iso-8859-1
Date: Thu, 24 Jul 2008 21:11:22 +0200 (CEST)
MIME-Version: 1.0


Sent to CCL by: "Sten Nilsson Lill" [stenil+*+chem.gu.se]
Hello René and Flavio,

you can do something similar with the Chemcraft program
(http://www.chemcraftprog.com). When animating the imaginary frequency in
the program you can freeze the structure at the "end-points" of the
vibration and thus get two sets of new coordinates for starting
calculations for finding the two minima on each side of the TS.

Hope this helps,

Sten





>
> Sent to CCL by: René Kanters [rkanters++richmond.edu]
> Hi Flavio,
>
> I hacked together a little perl scrip that will look at the first set
> frequency information in a gaussian calculation and generate a new
> set of xyz coordinates in which the structure is moved along a
> vibrational coordinate for a certain amount (see the command line
> arguments in the script below).
>
> Note that it may be necessary, depending on the symmetry of the
> saddlepoint you got to create a new input with going in the positive
> and another one in the negative direction of the imaginary frequency
> since you can't be sure which one will lead you to a lower minimum.
>
> I hope this helps.
>
> René
>
> PS it's not pretty (I am not a perl programmer), but it has worked
> for me.
>
> #! /usr/bin/perl
> ###############################################
> # script to take a gaussian log file output and generate structure
> # information (cartesian) for a new structure with a displacement
> # along a frequency coordinate in the direction along the '-v' vibration
> # for a displacement of '-d' times the vibrational vector
> #
> # command line arguments:
> #
> # -h        : prints help and quits.
> # -d float  : displacement along vibrational mode default 0.1
> # -v int    : vibration number to use default 1
> # required : filename (only sees last one)
> ################################################
>
> #
> $test = 0;  # for debugging purposes (prints out extra stuff)
>
> # set up the defaults
> $vibration = 1;
> $displacement = 0.1;
> $file = "";
>
> # 'constants' not using the 'use constant NAME => value;' method.
> $C_STRUCTURE = "Standard orientation:";
> $C_ENDSTRUCTURE = "---------";
> $C_FREQUENCY = "Frequencies --";
>
> while ($#ARGV >= 0) {
>    if ($ARGV[0] eq "-d")    { $displacement = $ARGV[1]; shift ]*[ARGV; }
>    elsif ($ARGV[0] eq "-v") { $vibration = $ARGV[1]; shift ]*[ARGV; }
>    elsif ($ARGV[0] eq "-h") { &usage(); exit;}
>    else { $file = $ARGV[0];}
>    shift ]*[ARGV;
> }
>
> if ($file eq "") { &usage(); exit;}
>
> open(IN,$file) || die "Could not open file '$file'.\n";
>
> while (1) {
>    # read until I get a structure (should happen first) or a frequency
>    until ($_ = <IN>, $_ =~ /$C_STRUCTURE/ or $_ =~ /$C_FREQUENCY/ or
> eof) { }
>    if ($_ =~ /$C_STRUCTURE/) {  # READ THE STRUCTURE
>      $nat = -1;   # reset the atom index counter : only need last
> structure
>      $at = ();    # clear out the arrays of atomnumber, x, y and z
>      $x = ();
>      $y = ();
>      $z = ();
>      skiplines(4); # position read line to first atom in the list
>      while ($_ = <IN> and not $_ =~ /$C_ENDSTRUCTURE/ ) {
>        ]*[tokens = split(' ', $_);
>        $nat++;
>        $at[$nat] = $tokens[1];
>        $xind = $#tokens - 2; # needed if the atomic type is missing
> (happens sometimes).
>        $x[$nat] = $tokens[$xind];
>        $y[$nat] = $tokens[$xind+1];
>        $z[$nat] = $tokens[$xind+2];
>      }
>    } elsif ($_ =~ /$C_FREQUENCY/) { # READ THE FREQUENCY INFORMATION
>      # since there are three vibrations per line, I can determine how
>      # many of these I need to skip before I can read the frequency I
> need.
>      $skipsize = 4 + ($nat+1) + 3;  # skip rest header, vibrations
> and start header
>      for ($i=0; $i<int($vibration/3); $i++) { skiplines($skipsize); }
>
>      skiplines(4);
>      $xind = 2 + (($vibration-1) % 3) * 3; # position in the tokens
> of vib vector
>      if ($test eq 1) { print "vibration = $vibration, xind = $xind\n"; }
>      for ($i=0;$i<=$nat;$i++) {
>        $_ = <IN>;
>        ]*[tokens = split(' ',$_);
>        if ($test eq 1 ) {
>          print "input $_";
>          print "($x[$i],$y[$i],$z[$i]) + $displacement x ($tokens
> [$xind],$tokens[$xind+1],$tokens[$xind+2])\n";
>        }
>        printf "%4d  % .6f  % .6f  % .6f\n",$at[$i], $x[$i]+
> $displacement*$tokens[$xind], $y[$i]+$displacement*$tokens[$xind+1],
> $z[$i]+$displacement*$tokens[$xind+2];
>      }
>      exit; # AND WE ARE DONE!!!!
>    } elsif (eof) { close IN; exit; }
> }
>
> ##################################################
> # skiplines : argument n: number of lines to skip
> ##################################################
> sub skiplines {
>    local $n, $i;
>    $n = shift(]*[_);
>    for ($i=0;$i<$n;$i++) { <IN> || die "skiplines encountered EOF."; }
> }
>
>
> ##################################################
> # usage prints a message about how to use sp2g03
> ##################################################
> sub usage {
> print <<ENDUSAGE;
> Usage: nfreq [-h] [-d displacement] [-v vibrationnnumber] filename
>
> -d : displacement step along vibrational mode default 0.1
> -v : index of vibrational mode to follow default 1
> -h : prints this help
>
> Will create the structure '-d' along the '-v'th vibrational mode of
> the stucture.
> ENDUSAGE
> }
>
> On Jul 23, 2008, at 3:39 PM, flavio forti fforti.:.fortisrl.com.ar
> wrote:
>
>>
>> Sent to CCL by: "flavio  forti" [fforti^_^fortisrl.com.ar]
>> Hi everybody. I am trying to optimize a large set of histamine
>> monocation  conformers in solution (PCM) with B3LYP/6-31G*. I had
>> some which converged to a saddle point (1 imaginary frequency) but
>> finally, after several reoptimizations with CalcFC they arrived to
>> a minimum. But there is one still resisting. CalcAll would be to
>> expensive, what do you suggest?
>> thanks
>> flavio
>>
>>
>>
>> -= This is automatically added to each message by the mailing
>> script =-
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>>
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>
>


Ph. D. Sten Nilsson Lill
Dep. of Chemistry
Göteborg University
Kemigĺrden 4
S-412 96 Göteborg, Sweden
Phone: +46-31-772 2901
Fax: +46-31-772 3840
E-mail: stenil_-_chem.gu.se
Alternative e-mail: slill1_-_lsu.edu