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Eric Pettersen pett at cgl.ucsf.edu
Tue Mar 29 10:44:55 PDT 2011

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 Pettersen
                         UCSF Computer Graphics Lab

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"  
> Failure running ANTECHAMBER for residue ARA
> Check reply log for details
> -- 
> Zhaoyang Ding
> East China University of science and technology
> Shanghai China
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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