AMBER Archive (2009)

Subject: Re: [AMBER] Antechamber: stuck at bondtype

From: Ye MEI (ymei_at_itcc.nju.edu.cn)
Date: Wed Jun 17 2009 - 08:48:18 CDT

maybe you want to try openbabel.

Ye

On 6/17/2009, "Jack Shultz" <js_at_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_at_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
>
>_______________________________________________
>AMBER mailing list
>AMBER_at_ambermd.org
>http://lists.ambermd.org/mailman/listinfo/amber
>
>

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber