read parameters of metal ions

[Anonymous]

Hi!

How can I read parameters of several metal ions, solvent molecules or ligands?

When I try to run this:
from rosetta import *
init()
params_list=Vector1()
res_set = generate_nonstandard_residue_set(params_list)

I get the following error:
…
In [4]: res_set = generate_nonstandard_residue_set(params_list)
core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 7533 residue types

ERROR: Residue names must be unique!
ERROR:: Exit from: src/core/chemical/ResidueTypeSet.cc line: 358

---

RuntimeError Traceback (most recent call last)

/data/mcm/henricsn/sysmolab/results/2011-07_LmPYK/ in ()

/scratch/mcm/henricsn/lib/PyRosetta/rosetta/__init__.pyc in generate_nonstandard_residue_set(params_list)
206 res_set.read_files(params_list, ChemicalManager.get_instance().atom_type_set(“fa_standard”),
207 ChemicalManager.get_instance().mm_atom_type_set(“fa_standard”),
–> 208 ChemicalManager.get_instance().orbital_type_set(“fa_standard”),
209 )
210 return res_set

RuntimeError: unidentifiable C++ exception

The paramfiles MG.params SO4.params K.params are in the same directory (attachment).
Thanks for your help.

Stefan

[Anonymous]

Well, as it says, residue names must be unique. One of your added ones is clashing with an existing one, or you’re managing to add them twice.

I would guess it’s magnesium, given that that’s already in the default residue type set. My second guess would be that it’s a K-potassium versus K-lysine conflict.

[Anonymous]

The problem of reading metal ions was coming from the spacing in the PDB file. The same problem was already posted in http://www.rosettacommons.org/content/some-application-troubles-when-using-resfile-flag

Here is a sample script and a test pdbfile with correct spacing:

from rosetta import *
init()
params_list=Vector1()
res_set = generate_nonstandard_residue_set(params_list)
p=Pose()
pose_from_pdb(p, "test.pdb")


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