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PostPosted: Tue Mar 19, 2013 6:07 am 
Millimolar User
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Joined: Mon Feb 18, 2013 7:47 am
Posts: 1
i have a list of 25 molecules (just for tutorial) in pdb format. I am trying to convert them into pdbqt format using the following script:

for f in CID_*.pdb
echo $f
/home/kamaneeya/MGLTools-1.5.4/MGLToolsPckgs/AutoDockTools/Utilities24/ -l $f

but if i run it I am getting the following error for almost all the molecules:
Unable to assign MAP type to atom N
Sorry, there are no Gasteiger parameters available for atom CID_*****: :LIG1:N
WARNING: 23 atoms of 30 in CID_*****.pdb were not written

does this mean the pdbqt files are not properly done? Will I be able to use them for virtual screening using autodock vina?
If I am trying to view them in ADT I am not able to see anything and its giving me an error message. But if I try to view in PYMOL viewer I can see the file normally. What should I do?
If this script works I have to use it on a huge library of molecules for virtual screening. Please help me as soon as possible..

Thanks a lot :)

Last bumped by kamaneeya on Tue Mar 19, 2013 6:07 am.

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