AMBER Archive (2006)

Subject: RE: AMBER: Problem with bcc flag of antechamber

From: Junmei Wang (jwang_at_encysive.com)
Date: Thu Jul 06 2006 - 12:53:37 CDT

Here is the basic rule:
 
If AMBERHOME is set and "-df" is 1 (the default), divcon is used; if
AMBERHOME is not set and ACHOME is set, mopac.sh in $ACHOME/exe is used;
if both environment strings are set, divcon is applied for "-df" to be
set to 1 and mopac.sh for "-df" to be set to 0; if neither environment
string is set, mopac.sh must be in the current working directory to use
the "-c bcc" flag.
 
The following is the sample of mopac.sh
 
#!/bin/sh
 
# Edit the following to match your local environment; the syntax
# for calling this shell script should be: mopac.sh input output.
# Depending on which version of mopac you have, you may need to remove
# the "<" and ">" symbols below, or make other changes. For example,
# some versions of mopac expect the input file to be "FOR005" and the
# output to be "FOR006"; some versions require the input file to end in
# ".DAT", etc., etc.
 
ln mopac.in FOR005
$ACHOME/exe/mopac
mv FOR006 mopac.out
rm -f FOR0??

All the best

Junmei

 

==================================================
Dr. Junmei Wang
Chemistry & Biophysics
Encysive Pharmaceuticals Inc.
7000 Fannin, Houston TX 77030
Tel: 713-578-6649
Email: jwang_at_encysive.com
http://amber.scripps.edu/antechamber/antechamber.html
==================================================

        -----Original Message-----
        From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu]
On Behalf Of Gobind Bisht
        Sent: Thursday, July 06, 2006 12:01 PM
        To: amber_at_scripps.edu
        Subject: AMBER: Problem with bcc flag of antechamber
        
        
        Hi all,
               i'm sry if my questions are preliminary but i'm new with
AMBER. Is it complsory for me to install MOPAC to use the bcc flag in
creating the prepin file for a charged molecule. If yes then will te
simple installation do the task or ineed to do something else also (liek
setting environment variable etc.). This is for AMBER 9 installed on
Fedora core3. Also when i compiled AMBER using the intel fcc,ccp and MKL
libraries evrything got installed except for leap. what is this problem
due to. I'm attaching an error log. Please help..
        thanx a lot in advance
        you are being very helpful
        
        Gobind Singh Bisht
        Btech II yr, Department Of Biotechnology
        IIT Kharagpur, Kharagpur-721302
        West Bengal,
        

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