ligand dock into HEM containg pdb

[Anonymous]

 Hi all

 I would like to dock  unknown chemical into PDB which have HEM as a cofactor

 But I want to fix the HEM molecule fixed during docking with constraint statement below

                 <RESIDUE_SELECTORS>

                        <ResidueName name=”HEM” residue_names=”HEM” residue_name3=”HEM” />

                </RESIDUE_SELECTORS>

.

.

.

                <MOVERS>

                        <VirtualRoot name=”HET” removable=”1″ remove=”0″ />

                        <AddConstraints name=”add_coord_csts” >

                                <CoordinateConstraintGenerator name=”coord_cst_gen” residue_selector=”HEM” sd=”1.0″/>

                        </AddConstraints>

 

But when I do the docking with above xml  I got the following warning which means that constraints are not working.

protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER AddConstraints – add_coord_csts=======================

protocols.constraint_generator.CoordinateConstraintGenerator: [ WARNING ] Adding coordinate constraints to a pose without a virtual root – results may not be as expected.

protocols.constraint_generator.AddConstraints: ConstraintGenerator named coord_cst_gen did not generate any constraints. Not adding anything.

 

I totally stuck in this problem

I have two questiion

first, In the rosetta manual, it is written that  for constraints to have an effect,  the coordinate_constraint scoreterm must be on in the scorefunction.

how can I add constraint scoreterm to my scorefunction?

here is definition of my scorefunction

                <SCOREFXNS>

                        <ScoreFunction name=”ligand_soft_rep” weights=”ligand_soft_rep”>

                        </ScoreFunction>

                        <ScoreFunction name=”hard_rep” weights=”ligand”>

                        </ScoreFunction>

                </SCOREFXNS>

 

second,  As the warning says, it seems that to add constraints require virual root.  Does anybody know how to add virtualroot in my xml file?

there is an explanation about virtual root in rosetta manual

https://new.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Movers/movers_pages/VirtualRootMover

But I don’t know how to add virtual root with this manual.

Any kind of suggestion or comment would be really appreciated

Thanking in advance

 

 

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