ADL: Missing Atoms

Arun Kumar arunkumar.thangaraju at gmail.com
Sun May 7 02:46:35 PDT 2006


Friends,
I have a strange problem in my pdb file. When I convert the pdb file to pdbq
format using pmolq I get missing atoms in a few residues. Upon running
autogrid with the same pdbq i got the following error

../../autodock/bin/i86Linux2/autogrid3: WARNING!  Atom type error, can't
find type for "2LPG" in typelist "CNOSHXM".

../../autodock/bin/i86Linux2/autogrid3: WARNING!  Atom type error, can't
find type for "1LPD" in typelist "CNOSHXM".

../../autodock/bin/i86Linux2/autogrid3: WARNING!  Atom type error, can't
find type for "2LPD" in typelist "CNOSHXM".

../../autodock/bin/i86Linux2/autogrid3: WARNING!  Atom type error, can't
find type for "1LPD" in typelist "CNOSHXM".

../../autodock/bin/i86Linux2/autogrid3: WARNING!  Atom type error, can't
find type for "2LPD" in typelist "CNOSHXM".

../../autodock/bin/i86Linux2/autogrid3: WARNING!  Atom type error, can't
find type for "1LPD" in typelist "CNOSHXM".


The List goes on. How to rectify it?  The glg file got created but the other
files such as map.fld, .xyz were not created. Upon running autodock3
[arun at localhost 1pxx]$ ../../autodock/bin/i86Linux2/autodock3 -p
deracoxib.1pxx.dpf -l deracoxib.1pxx.dlg

../../autodock/bin/i86Linux2/autodock3: I'm sorry; I can't find or open "
1pxx.maps.fld"
__________________

It would be of great help if someone can suggest me .

Thank You
Arunkumar Thangaraju


More information about the autodock mailing list