ADL: autodock Digest, Vol 26, Issue 4

SUHAS VL suhasvl at gmail.com
Sun May 7 20:55:59 PDT 2006


hai

you can use rem-lp command to delete all the lone pair atom type.

This commnad is available in autodock

check it ,hope this will serve the purpose

suhas

On 5/8/06, autodock-request at scripps.edu <autodock-request at scripps.edu>
wrote:
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> Today's Topics:
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>    1.  Missing Atoms (Arun Kumar)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 7 May 2006 15:16:35 +0530
> From: "Arun Kumar" <arunkumar.thangaraju at gmail.com>
> Subject: ADL: Missing Atoms
> To: autodock at scripps.edu
> Message-ID:
>         <7a1df42a0605070246h445a881byc008acc383e63298 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> 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
>
>
> ------------------------------
>
> ________________________________________________
> --- ADL: AutoDock List  ---
> http://www.scripps.edu/pub/olson-web/doc/autodock/ ---
>
> End of autodock Digest, Vol 26, Issue 4
> ***************************************
>


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