On Mon, Apr 05, 2010, monica.imtech.res.in wrote:
>
> antechamber -i plp.pdb -fi pdb -o plp.mol2 -fo mol2 -c bcc -s 2
>
> i got the following error:
> Running: $AMBERHOME/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o
> ANTECHAMBER_BOND_TYPE.AC -f ac -j full
> Warning: the assigned bond types may be wrong, please :
> (1) double check the structure (the connectivity) and/or
Item (1) is usually the cause of the problem. Have you visually inspected
your structure to insure that it looks OK and that all hydrogens are present
in the proper locations?
> -bash: reduce: command not found
This suggests that you have not sucessfully installed AmberTools.
> then i tried to add hyrogens using pymol and got the file and tried to give
> antechamber command as aboveo
Again, you need to check item (1) above. Antechamber needs fairly "good"
input structures.
...good luck....dac
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Received on Mon Apr 05 2010 - 05:00:02 PDT
