On Mon, May 14, 2012, Pedro Swagger wrote:
>
> I use antechamber but I got the following error: Any idea??????
>
> antechamber -i sulfate.pdb -fi pdb -o sulfate.mol2 -fo mol2 -c bcc -s 2
>
>
> *Error: cannot run "/home/pedro/Programs/amber11/bin/bondtype -j full -i
> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in
> judgebondtype() of antechamber.c properly, exit*
Look carefully at your input structure, although I suspect something called
"sulphate" might be pretty simple. Use the "acdoctor" program to check for
common problems. If this really is sulphate ion, you need to use the -nc
flag to tell the program that the net charge is -2: if not told otherwise,
antehcamber assumes that the input molecule is neutral.
....dac
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Received on Mon May 14 2012 - 16:00:04 PDT
