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ding kevin dingzhaoyang87 at gmail.com
Tue Mar 29 01:20:28 PDT 2011

Hi, I am a freshman to use Chimera. When I run "add charge" of ligand by the
tutorial, and the error below appears. I would like to know the reasons and
how could I solve this problem.

Thank you very much!

Charge model: AMBER ff99SB
Assigning partial charges to residue ARA (net charge +0) with am1-bcc method
Running ANTECHAMBER command: D:/drivers/Chimera
1.5.3rc/bin/amber11/bin\antechamber -ek qm_theory='AM1', grms_tol=0.02,
tight_p_conv=0, scfconv=1.d-10, -i
c:\users\dingzh~1\appdata\local\temp\tmpkghulj\ante.in.mol2 -fi mol2 -o
c:\users\dingzh~1\appdata\local\temp\tmpkghulj\ante.out.mol2 -fo mol2 -c bcc
-nc 0 -j 5 -s 2
(ARA) cygwin warning:

(ARA)   MS-DOS style path detected:

(ARA)   Preferred POSIX equivalent is:

(ARA)   CYGWIN environment variable option "nodosfilewarning" turns off this

(ARA)   Consult the user's guide for more details about POSIX paths:

(ARA)     http://cygwin.com/cygwin-ug-net/using.html#using-pathnames

(ARA) /usr/bin/antechamber.exe: error while loading shared libraries: ?:
cannot open shared object file: No such file or directory

(ARA) Error: cannot run ""D:/drivers/Chimera
1.5.3rc/bin/amber11/bin/bondtype" -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o
ANTECHAMBER_BOND_TYPE.AC -f ac" in judgebondtype() of antechamber.c
properly, exit

(ARA) Running: "D:/drivers/Chimera 1.5.3rc/bin/amber11/bin/bondtype" -j part

Failure running ANTECHAMBER for residue ARA
Check reply log for details

Zhaoyang Ding
East China University of science and technology
Shanghai China
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