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: c:\users\dingzh~1\appdata\local\temp\tmpkghulj\ante.in.mol2 (ARA) Preferred POSIX equivalent is: /cygdrive/c/users/dingzh~1/appdata/local/temp/tmpkghulj/ante.in.mol2 (ARA) CYGWIN environment variable option "nodosfilewarning" turns off this warning. (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 -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac Failure running ANTECHAMBER for residue ARA Check reply log for details -- Zhaoyang Ding East China University of science and technology Shanghai China
Hi Zhaoyang, So far I have been unable to reproduce your problem here. Could you please use the "Report A Bug" item (in the Help menu) to submit a bug report for this? Using Report A Bug will provide me more information, such as what version of Chimera you're using and what version of Windows, that will help me track this down. Thanks! --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Mar 29, 2011, at 1:20 AM, ding kevin wrote:
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: c:\users\dingzh~1\appdata\local \temp\tmpkghulj\ante.in.mol2
(ARA) Preferred POSIX equivalent is: /cygdrive/c/users/dingzh~1/ appdata/local/temp/tmpkghulj/ante.in.mol2
(ARA) CYGWIN environment variable option "nodosfilewarning" turns off this warning.
(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 -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
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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participants (2)
-
ding kevin -
Eric Pettersen