Modeling small molecules

[Anonymous]

Hi all,

Just trying to model a small molecule and how it interacts w/ my bigger protein in pyrosetta. 

 

I got this far: 

 

pose2 = Pose()

nonstandard_residue_set = generate_nonstandard_residue_set(pose2, [“ARA2.params”])

pose = pose_from_pdb(nonstandard_residue_set, “combine.pdb”)

But pose_from_pdb only takes only 1 argument, how do I get around this? 

 

[Anonymous]

In very broad terms, two options:

1) have the small molecule already present in your PDB file.  The coordinates won’t matter so long as you plan to correct/modify them later.

 

2) create a Residue object of your small molecule and attach (I don’t remember the function name, it’s probably append) it to the Pose that contains the protein. 

[Anonymous]

The pose_from_pdb() function is a bit of a quick wrapper around the more general pose_from_file() function. The pose_from_file() function has a number of different signatures, but one of them is pose_from_file( ResidueTypeSet, filename ).

The other way to do it (and potentially the preferred way in this case) is to read the file into an existing Pose which contains the modified ResidueTypeSet   — pose_from_file( pose, filename ). — (The reason why generate_nonstandard_residue_set() takes a pose is that it annotates that Pose’s ResidueTypeSet to contain the particular residues added. The modified residue type set is then attached to that pose.)

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