Hello,
I'm new to Amber as well as Ubuntu. I experienced a Problem and don't
know how to solve it.
I want to use antechamber to write a mol 2 file of a small molecule with
informations about charges and so on. The Ligand is a pdb file.
I came as far as
$AMBERHOME/bin/antechamber
Usage: antechamber -i input file name
-fi input file format
-o output file name and so on...
so i think the program works, at least the test after the instalation
did - with one exception out of 499... but i remember a comment telling
me this is expected.
if type:
$AMBERHOME/bin/antechamber -i yxz.pdb -fi pdb -o xyz.mol2 -fo mol2 -c
bcc -s 2
I get
Cannot open the input file:xyz.pdb in rpdb(), exit
I copied the file to many folders because i thougt maybe the program
looks in "the wrong place". I also tested to do this with the
sustiva.pdb from the tutorial and got the same result, so i think its
not the file but something else.
Is there a working directory, if yes, where is it? Can i tell
antechamber where to look for a file? Or do i've another problem?
Thanks
Best regards
Matthias
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Received on Wed Feb 13 2013 - 11:00:03 PST
