It is advised to open the crystal structure or the protein in UCSF Chimera, an open source GUI compatible with Windows, Mac and Linux which can be efficiently used to remove waters and any other non-standard residues. Then save the PDB and use it for docking. It is the best practice.

Cheers!!

SB

Can you please describe us, how did you remove HOH molecules?

I would like to know what did you do step by step....

and

Is your protein a homology modeled pdb file?

Regards,

1. Open any crystal structure in Chimera (for example PDB: 3U1I)

2. Go to Select>>Residue>click on HOH (or any other nonstandard residues you want to delete)

3. Go to Actions>>Atoms/Bonds>>delete (it will delete the selected HOH from the PDB)

4. Then save it by clicking File>>Save PDB

Play around it is easy. Hope it helps.

Best wishes,

SB

Chimera is a good software but For easy purpose download discovery studio visualizer and in that tool easily you can remove water atoms.

Even u can remove water molecules of a pdb file manually..

just by opening it with a text editor and deleting all the HOH atomtype entries of water molecule....then save the pdb file. :)

"NO new selection" means that there are no water molecule entry in the pdb file...

Open the PDB file with Wordpad. Go to HETATM which includes the Ligands, ions and water molecules. Selectively delete all the HOH.

Outline of PDB: (Excluding BRANCH, ENDBRANCH & REMARKS)

ATOM

TER

HETATM

TER

END

One easy/lazy way is to get yourself a copy of pymol and in the main menu "Remove Waters", then re-save.

Select MENU: select from String select HOH

then

Edit menu:  delete selected molecule.

linux os

sed -i '/HOH/d' xxx.pdb

you can easily open your pdb file with word office and delete water inside it manually. select the final "HOH" atoms and delete them.  

thanks all of u for ur suggestion