maybe you want to try openbabel.
Ye
On 6/17/2009, "Jack Shultz" <js.drugdiscoveryathome.com> wrote:
>I am trying to convert a pdb file to mol2 using antechamber. The
>example from the tutorial 5 seems to work ok (sustiva.pdb)
>The current pdb I am trying to convert just gets stuck at the
>bondtype. There are about 110 residues in this protein. It was derived
>from a docking complex using Autodock Tools. For testing purposes I
>also tried antechamber on the original pdb file used as the receptor
>and that had the same issue.
>
>[boincadm.vps receptor]$ antechamber -fi pdb -i
>receptor_ligand_0.pdbqt -fo mol2 -o receptor_ligand_0.mol2 -s 2
>
>The atom number exceeds the MAXATOM, reallocate memory
>Info: the bond number exceeds MAXBOND, reallocate memory automatically
>Running: /usr/local/antechamber-1.27/exe/bondtype -i
>ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full
>
>
>--
>Jack
>
>http://drugdiscoveryathome.com
>http://hydrogenathome.org
>
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>
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Received on Mon Jul 06 2009 - 09:54:19 PDT
