#! /usr/bin/per= l

###############= ################################

# script to tak= e a gaussian log file output and generate structure

# information (= cartesian) for a new structure with a displacement

# along a frequ= ency coordinate in the direction along the '-v' vibration

# for a displac= ement of '-d' times the vibrational vector

# command line = arguments:

# -h &nb= sp; : prints help and quits.

# -d float &nbs= p;: displacement along vibrational mode default 0.1

# -v int = : vibration number to use default 1

# required : fi= lename (only sees last one)

###############= #################################

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

# set up the de= faults

$vibration =3D = 1;

$displacement = =3D 0.1;

$file =3D "= ;";

# 'constants' n= ot using the 'use constant NAME =3D> value;' method.

$C_STRUCTURE = =3D "Standard orientation:";

$C_ENDSTRUCTURE= =3D "---------";

$C_FREQUENCY = =3D "Frequencies --";

while ($#ARGV &= gt;=3D 0) {

if ($ARG= V[0] eq "-d") { $displacement =3D $ARGV[1]; shift /a\A= RGV; }

elsif ($= ARGV[0] eq "-v") { $vibration =3D $ARGV[1]; shift /a\ARGV; }=

elsif ($= ARGV[0] eq "-h") { &usage(); exit;}

else { $= file =3D $ARGV[0];}

shift /a\A= RGV;

}

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

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

while (1) {

# read u= ntil I get a structure (should happen first) or a frequency

until ($= _ =3D <IN>, $_ =3D~ /$C_STRUCTURE/ or $_ =3D~ /$C_FREQUENCY/ or eof) = { }

if ($_ = =3D~ /$C_STRUCTURE/) { # READ THE STRUCTURE

$= nat =3D -1; # reset the atom index counter : only need last structur= e

$= at =3D (); # clear out the arrays of atomnumber, x, y and z

$= x =3D ();

$= y =3D ();

$= z =3D ();

s= kiplines(4); # position read line to first atom in the list

w= hile ($_ =3D <IN> and not $_ =3D~ /$C_ENDSTRUCTURE/ ) {

&= nbsp; /a\tokens =3D split(' ', $_);

&= nbsp; $nat++;

&= nbsp; $at[$nat] =3D $tokens[1];

&= nbsp; $xind =3D $#tokens - 2; # needed if the atomic type is missing (happe= ns sometimes).

&= nbsp; $x[$nat] =3D $tokens[$xind];

&= nbsp; $y[$nat] =3D $tokens[$xind+1];

&= nbsp; $z[$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 need.

$= skipsize =3D 4 + ($nat+1) + 3; # skip rest header, vibrat= ions and start header

f= or ($i=3D0; $i<int($vibration/3); $i++) { skiplines($skipsize); = }

&n= bsp;

s= kiplines(4);

$= xind =3D 2 + (($vibration-1) % 3) * 3; # position in the tokens of vib = vector

i= f ($test eq 1) { print "vibration =3D $vibration, xind =3D $xind\n&quo= t;; }

f= or ($i=3D0;$i<=3D$nat;$i++) {

&= nbsp; $_ =3D <IN>;

&= nbsp; /a\tokens =3D split(' ',$_);

&= nbsp; if ($test eq 1 ) {

&= nbsp; print "input $_";

&= nbsp; print "($x[$i],$y[$i],$z[$i]) + $displacement x ($tok= ens[$xind],$tokens[$xind+1],$tokens[$xind+2])\n";

&= nbsp; }

&= nbsp; 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];

e= xit; # AND WE ARE DONE!!!!

} elsif = (eof) { close IN; exit; }

}

###############= ###################################

# skiplines : a= rgument n: number of lines to skip

###############= ###################################

sub skiplines {=

local $n= , $i;

$n =3D s= hift(/a\_);

for ($i= =3D0;$i<$n;$i++) { <IN> || die "skiplines encountered= EOF."; }

}

###############= ###################################

# usage prints = a message about how to use sp2g03

###############= ###################################

sub usage {

print <<E= NDUSAGE;

Usage: nfreq [-= h] [-d displacement] [-v vibrationnnumber] filename

-d : displaceme= nt step along vibrational mode default 0.1

-v : index of v= ibrational mode to follow default 1

-h : prints thi= s help

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

ENDUSAGE=

}

On May 8, 2013, at 3:58 PM, Anjan Roy aroy6|,|uic.edu wrote:

Sent to CCL by: "Anjan Roy" [aroy6!^!uic.edu]
Hello,

My Gaussian 09 opimization returns a negative frequency, one solution sugge= sted
was to distort the molecule in the direction if the negative freq motion. C= ould
someone kindly suggest how I can do this by subtracting structures in the <= br> command line or by way of a GUI.

thank you

Anjan

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--_000_A526E77202134A69BCAE22C6E72F66BDrichmondedu_-- From owner-chemistry@ccl.net Thu May 9 08:20:00 2013 From: "AMAN Gill emmie.aulakh_._gmail.com" To: CCL Subject: CCL:G: electrostatic potential conflict Message-Id: <-48664-130509081729-30422-seeIlcL0liXAWLhiawBCTg:+:server.ccl.net> X-Original-From: "AMAN Gill" Date: Thu, 9 May 2013 08:17:27 -0400 Sent to CCL by: "AMAN Gill" [emmie.aulakh\a/gmail.com] Hey everyone I have been working with gaussian. I have optimized dimethyl sulfide using Gaussian09. Gauss view indicates positive charge on S(+0.151) and the Hs (+0.201). However the molecular electrostatic map (using MOLEKEL)indicates negative electrostatic potential on Hs. Can anyone tell me why is this so? From owner-chemistry@ccl.net Thu May 9 10:47:00 2013 From: "Hanane Louanas hananelouanas]~[yahoo.fr" To: CCL Subject: CCL: scrf=(smd, dovacuum);scrf=(smd, solvent=water) results are identical! Message-Id: <-48665-130509104554-28950-B1aFy3GvM+HGoN+8TLPWJQ[-]server.ccl.net> X-Original-From: "Hanane Louanas" Date: Thu, 9 May 2013 10:45:53 -0400 Sent to CCL by: "Hanane Louanas" [hananelouanas .. yahoo.fr] I perform two types of calculations on the same starting , with scrf=(smd, dovacuum) and scrf=(smd, solvent=water) ,surprisingly! , all results of structural and energtic delta are identical!! you opinion will be helpful. Best regards, H.Louanas From owner-chemistry@ccl.net Thu May 9 12:21:00 2013 From: "Hao-Bo Guo guohaobo^gmail.com" To: CCL Subject: CCL: scrf=(smd, dovacuum);scrf=(smd, solvent=water) results are identical! Message-Id: <-48666-130509121948-30870-WrbFEJdcNKR4zhkWnAt2bw()server.ccl.net> X-Original-From: Hao-Bo Guo Content-Type: multipart/alternative; boundary=047d7bdc0982f8bd7904dc4b6abb Date: Thu, 9 May 2013 12:19:42 -0400 MIME-Version: 1.0 Sent to CCL by: Hao-Bo Guo [guohaobo{=}gmail.com] --047d7bdc0982f8bd7904dc4b6abb Content-Type: text/plain; charset=ISO-8859-1 They should be the same. The default solvent for scrf is water, you do not need to specify it; although the default is skipvacuum, dovacuum is used only to perform a vacuum single point calculation to compare with the aqueous result, such that the solvation free energy deltaG could be obtained. But dovacuum should not affect the scrf calculation. If you want to do optimization etc in vacuum, simply dismiss the scrf keyword. On Thu, May 9, 2013 at 10:45 AM, Hanane Louanas hananelouanas]~[yahoo.fr < owner-chemistry ~ ccl.net> wrote: > > Sent to CCL by: "Hanane Louanas" [hananelouanas .. yahoo.fr] > I perform two types of calculations on the same starting , with scrf=(smd, > dovacuum) and scrf=(smd, solvent=water) ,surprisingly! , all results of > structural and energtic delta are identical!! you opinion will be helpful. > > Best regards, > H.Louanas> > > --047d7bdc0982f8bd7904dc4b6abb Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

They should be the same. The default solvent for scrf is w= ater, you do not need to specify it; although the default is skipvacuum, do= vacuum is used only to perform a vacuum single point calculation to compare= with the aqueous result, such that the solvation free energy deltaG could = be obtained. But dovacuum should not affect the scrf calculation. If you wa= nt to do optimization etc in vacuum, simply dismiss the scrf keyword.

On Thu,= May 9, 2013 at 10:45 AM, Hanane Louanas hananelouanas]~[yahoo.fr <owner-chemistry ~ ccl.net> wrote= :

Sent to CCL by: "Hanane =A0Louanas" [hananelouanas .. yahoo.fr]
I perform two types of calculations on the same starting , with scrf=3D(smd= ,
dovacuum) and scrf=3D(smd, solvent=3Dwater) ,surprisingly! , all results of=
structural and energtic delta are identical!! you opinion will be helpful.<= br>
Best regards,
H.Louanas

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--047d7bdc0982f8bd7904dc4b6abb-- From owner-chemistry@ccl.net Thu May 9 17:25:00 2013 From: "Nathan A. Seifert nas3xf*|*virginia.edu" To: CCL Subject: CCL:G: Gaussian09 -- problem with relaxed PES scan Message-Id: <-48667-130509164724-24461-Ei3E39QvJDuCFGkZrmOLdQ..server.ccl.net> X-Original-From: "Nathan A. Seifert" Date: Thu, 9 May 2013 16:47:23 -0400 Sent to CCL by: "Nathan A. Seifert" [nas3xf^_^virginia.edu] Hi to all, I am having some issues initializing a relaxed 2D PES scan for the acetylene- benzene system, in particular looking at the PES of the acetylene rotating/tilting normal to the plane of the benzene ring. Below is my Gaussian input file: =========== %nprocshared=4 # opt=modredundant m062x/6-311++g(d,p) nosymm ACETYLENE-BENZENE 0 1 X C 1 1.40098300 C 1 1.40098286 2 60.00002040 C 3 1.40098200 1 60.00002040 2 180.00000000 0 C 1 1.40098300 4 60.00002040 3 180.00000000 0 C 1 1.40098286 4 120.00004080 3 179.99971666 0 C 6 1.40098200 1 60.00002040 5 180.00000000 0 H 2 1.08668497 1 179.92349558 4 89.99985833 0 H 3 1.08668451 1 179.92382914 4 89.97993559 0 H 4 1.08668451 3 119.99992369 1 179.91204553 0 H 5 1.08668497 1 179.92349558 4 -89.99985833 0 H 6 1.08668451 1 179.92382914 4 -90.01978106 0 H 7 1.08668451 6 119.99992369 1 179.91204553 0 H 1 2.35138000 3 90.00000000 9 0.00000000 0 C 14 1.06664000 1 180.00000000 3 -169.45000000 0 C 15 1.21740000 14 180.00000000 1 172.30200000 0 H 1 5.70030000 3 90.00000000 9 -0.02000000 0 A 15 14 1 S 20 4.500000 D 15 14 1 3 S 20 4.50000 ============== When I run this, I get an error regarding atom 16 (the last carbon of the list). I think it has to do with the dihedral -- GaussView says the dihedral is infinite since the system is collinear. I'm not sure how to avoid this. Any suggestions would be greatly appreciated!!! Cheers, Nathan Seifert