Subject: the probelm for "pdbqtopdb" command in Autodock

From: "xiongying99" <xiongying99/at/fescomail.net>
Date: Mon, 15 Sep 2003 21:30:45 +0000

Dear sir,
 I am now using Autodock3.0. When I test the examples in autodock web 
file,(3PTB: Benzamidine docking to beta-Trypsin), I succeed in using 
autogrid, autotors and autodock command. I finally got the pdb file contains 
the docked conformations of the ligand. I want to add  the macromolecule and 
the docked conformations together into one PDB file that contains 
everything. I find the answer in the  FAQ (Frequently Asked Questions) page 
as following:
% get-dockings mydocking.dlg
% pdbqtopdb mymacromolecule.pdbqs >> mydocking.dlg.pdb
  However, when I run pdbqtopdb command, the error information is displayed:
 ---------------------------------------------------------- 

% pdbqtopdb 3ptb.pdbqs >> benA.3ptb.dlg.pdb
awk: /home/xiong/autodock/dist305/share/pdbtopdb2.awk:49: fatal: Invalid 
range end: /[0-9][+- ]/
/home/xiong/autodock/dist305/share/fixatomnames: line 8:  4340 M Ic
{_    
sed -f $AUTODOC
K_UTI/fixatomnames.sed $*
/home/xiong/autodock/dist305/share/getpdbrecords: line 2:  4338 M Ic
{_   
egrep "^ATOM|^
HETATM|^REMARK|^USER|^END |^TER|^MODEL |^ENDMDL" $*
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Could you please tell me why I can't get the pdb file contain the 
macromolecule and the docked ligand conformations?

   Thanks a lot ! 

        Yours Sincerely
    Ying Xiong (my email address: xiongying99/at/fescomail.net)

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