AMBER Archive (2003)

Subject: Re: AMBER: AM1-BCC in Amber7

From: Junmei Wang (JWang_at_encysive.com)
Date: Tue Nov 11 2003 - 15:49:31 CST

Hi, Joey,
I mopac.sh I used is like the following:

Best

Junmei
------------------------------------------------------------------------
For mopac7/mopac8

#!/bin/csh -f
set job = $1:r
foreach file (out log brz gpt esp ump arc syb end)
    if -e $job.$file rm $job.$file
end
if -e $2 rm $2

setenv FOR005 $1
setenv FOR006 $2
setenv FOR009 $job.res
setenv FOR010 $job.den
setenv FOR011 $job.log
setenv FOR012 $job.arc
setenv FOR013 $job.gpt
setenv FOR016 $job.syb
setenv FOR020 $job.ump
setenv SETUP SETUP.DAT
setenv SHUTDOWN $job.end

$AMBERHOME/exe/mopac_7_8.sgi $job <$1

if -e core rm core

--------------------------------------------------------------------------------
For mopac508mn

#!/bin/csh -f
if -e $2 rm $2
$ACROOT/exe/mopac508mn.sgi <$1 >$2
if -e core rm core

===============================================================
Dr. Junmei Wang
Chemistry & Biophysics
Encysive Pharmaceuticals
7000 Fannin, Houston TX 77030
Tel: 713-5786649
Email: jwang_at_tbc.com
Homepage: http://sigyn.compchem.ucsf.edu/members/jmwang/index.html
===============================================================

                                                                           
             Joey Harriman
             <s808o_at_unb.ca>
             Sent by: To
             owner-amber_at_scrip amber_at_scripps.edu
             ps.edu cc
                                                                           
                                                                   Subject
             11/10/2003 08:15 Re: AMBER: AM1-BCC in Amber7
             AM
                                                                           
                                                                           
             Please respond to
             amber_at_scripps.edu
                                                                           
                                                                           

I already have mopac downloaded and compiled for amber7...

-Joey

Quoting Ye Mei <ymei_at_itcc.nju.edu.cn>:

> you need download mopac and compile it.
> > Hi,
> >
> > I am trying to some AM1-BCC charge calculations in Amber7, but keep
getting error
> > messages. First, do you need to calculate charges in Gaussian when you
do the AM1
> > optimization (if so what method do people use)? Secondly, I am using
the
> following
> > input for antechamber and getting this error:
> >
> >
> > antechamber -i LIGAND_NO_H_AM1.out -fi gout -o ligand_no_H_am1bcc.mol2
-fo mol2 -c
> bcc
> >
> > Running: /usr/local/amber7/exe/mopac.sh ANTECHAMBER_MUL.MOP
ANTECHAMBER_MUL.OUT
> > Unable to find mopac charges in ANTECHAMBER_MUL.OUT
> >
> >
> > Am I using the correct input syntax in antechamber? Any advice would
be greatly
> > appreciated. Thanks in advance.
> >
> > Joey
> >
> > ----------------------------------
> > Joey Harriman
> > MSc Computational Chemistry
> > University of New Brunswick
> > Room 228
> > Toole Hall
> > s808o_at_unb.ca
> > 476-6543
> > ----------------------------------
> >
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber_at_scripps.edu
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> >
>
>
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>

----------------------------------
Joey Harriman
MSc Computational Chemistry
University of New Brunswick
Room 228
Toole Hall
s808o_at_unb.ca
476-6543
----------------------------------

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