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PostPosted: Mon Sep 07, 2009 9:57 am 
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Dear all,

i would like to insert one molecule of water during the docking process. To prepare the structures of the Target automatically, i use the prepare_receptor4.py script. Unfortunately, the script seem to remove the water molecule when creating the .pdbqt file. How to avoid this problem ? Can a water molecule be defined in the pdbqt format ?

Thanks.

Nicolas


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PostPosted: Mon Oct 05, 2009 2:08 am 
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If you run the script with the "-h" flag it will list the parameter settings. Under "cleanup type" (-U flag) the default is set to "nphs_lps_waters_nonstdres". the "waters" part sets the script to delete the water. I assume (but haven't actually run it) that resetting the -U flag to "nphs_lps_nonstdres" will keep your water molecule in the structure.

EDIT: I have tried this on a receptor file of mine. Two things: 1) including the "nonstdres" flag picked up the water as a non-standard residue and removed it. 2) I tried preparing this structure from ADT, which allowed keeping the water molecule, but could not compute a gastieger charge for the water. So I guess this solves the problem of keeping the water molecule physically in place, but won't help in using it as a H-bond donor/acceptor...which in my receptor is important.

tried to help but ended up needing help himself,
Bones


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PostPosted: Fri Oct 09, 2009 1:06 am 
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After a little bit of work, I have two solutions/observations.

1) working up a different crystal structure and leaving an ordered water using ADT seemed to function just fine. Looking at the resulting file showed the oxygen and both polar hydrogens explicitly stated in the pdbqt

Quote:
HETATM 4145 O HOH B 22 10.429 15.460 34.714 1.00 16.08 -0.411 OA
HETATM 4146 H1 HOH B 22 9.974 15.061 33.922 1.00 16.08 0.205 HD
HETATM 4147 H2 HOH B 22 11.376 15.211 34.523 1.00 16.08 0.205 HD


2) my solution to the first structure where ADT didn't seem to see the hydrogens as polar hydrogens was to simply add the atoms into the pdbqt file manually (manually = using a text editor) and setting the charges accordingly. AutoDock Vina didn't complain about this, the resulting structures looked reasonable enough, and I assume that it worked.

It is unclear why the water was properly recognized in one structure but not the other. I also have not attempted to work up the properly recognized structure using the python script.

bones


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