[AMBER] Antechamber - bug

From: Mahmoud A. A. Ibrahim <m.ibrahim.compchem.net>
Date: Thu, 24 Feb 2011 03:25:30 +0000

Dear AMBER
I am writing to inform you there is a bug (as I believe) in antechamber.
When I used antechamer to calculate the charge of a molecule I got an
error, with changing the charge calculation method from small to
capital case (or by writing the full method name instead of
abbreviation) it is working well. Here is the data:
******
:~/scratch> antechamber -i XXX.mol2 -fi mol2 -o LIG.mol2 -fo mol2 -j 1
-at amber -c cm1
Total number of electrons: 198; net charge: 0
Running: /software/amber10/bin/mopac.sh
Error: unable to find mopac charges in mopac.out
:~/scratch> antechamber -i XXX.mol2 -fi mol2 -o LIG.mol2 -fo mol2 -j 1
-at amber -c CM1
:~/scratch> antechamber -i XXX.mol2 -fi mol2 -o LIG.mol2 -fo mol2 -j 1
-at amber -c cm2
Total number of electrons: 198; net charge: 0
Running: /software/amber10/bin/mopac.sh
Error: unable to find mopac charges in mopac.out
:~/scratch> antechamber -i XXX.mol2 -fi mol2 -o LIG.mol2 -fo mol2 -j 1
-at amber -c CM2
:~/scratch> antechamber -i XXX.mol2 -fi mol2 -o LIG.mol2 -fo mol2 -j 1
-at amber -c bcc
Total number of electrons: 198; net charge: 0
Running: /software/amber10/bin/mopac.sh
Error: unable to find mopac charges in mopac.out
:~/scratch> antechamber -i XXX.mol2 -fi mol2 -o LIG.mol2 -fo mol2 -j 1
-at amber -c am1-bcc
:~/scratch> antechamber -i XXX.mol2 -fi mol2 -o LIG.mol2 -fo mol2 -j 1
-at amber -c mul
Total number of electrons: 198; net charge: 0
Running: /software/amber10/bin/mopac.sh
Error: unable to find mopac charges in mopac.out
:~/scratch> antechamber -i XXX.mol2 -fi mol2 -o LIG.mol2 -fo mol2 -j 1
-at amber -c Mulliken
:~/scratch>
*****
The commands were tested on different workstations having Amber10
version, all of them give the same results.
I am so sorry for any inconvenience caused if you are aware about it.
Sincerely;
M. Ibrahim

-- 
                  Mahmoud A. A. Ibrahim
                       Current Address
                 7.05, School of Chemistry,
              The University of Manchester,
         Oxford Road, Manchester, M13 9PL,
                       United Kingdom.
                        Home Address
                  Chemistry Department,
                     Faculty of Science,
                        Minia University,
                           Minia 61519,
                                Egypt.
                     Contact Information
           Email: m.ibrahim.compchem.net
              Website: www.compchem.net
                   Fax No.: +20862342601
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Feb 23 2011 - 19:30:04 PST
Custom Search