Member Site › Forums › PyRosetta › PyRosetta – General › read parameters of metal ions
- This topic has 2 replies, 2 voices, and was last updated 13 years, 4 months ago by Anonymous.
-
AuthorPosts
-
-
July 19, 2011 at 3:38 pm #981Anonymous
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 typesERROR: 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_setRuntimeError: unidentifiable C++ exception
The paramfiles MG.params SO4.params K.params are in the same directory (attachment).
Thanks for your help.Stefan
-
July 19, 2011 at 4:32 pm #5877Anonymous
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.
-
July 21, 2011 at 9:14 am #5884Anonymous
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")
-
-
AuthorPosts
- You must be logged in to reply to this topic.