dear Modellers,
I used MUTATE_MODEL to mutate ALA into ILE. now the ILE bumps into another residue. turning the dihedral of the ILE sidechain manually in a viewer will solve this. but I want to include an automatic minimization process in the mutate.top script, which will do it for me. In the FAQ section I saw the question 2. which describes a similar problem, it refers to examples/tutorial-model/model-segment.top . but it's not so clear to me how to merge the mutate.top and the model-segment.top in one both_steps.top, does it really need an alignment for doing this optimization of one residue?
thank you for good tips.
marc
On Wed, 13 Oct 2004 13:14:21 +0200 Marc Gasser marc.gasser@pharma.ethz.ch wrote:
dear Modellers, > > I used MUTATE_MODEL to mutate ALA into ILE. > now the ILE bumps into another residue. turning the dihedral > of the ILE sidechain manually in a viewer will solve this. but I > want to include an automatic minimization process in the > mutate.top script, which will do it for me. > In the FAQ section I saw the question 2. which describes a similar > problem, it refers to examples/tutorial-model/model-segment.top . > but it's not so clear to me how to merge the mutate.top and the > model-segment.top in one both_steps.top, does it really need an > alignment for doing this optimization of one residue? > > thank you for good tips. >
below is the top script I use, it's optimizing all residues instead of just selecting res 256. how can I restrict the optimization to residue 256?
# Mutate my_protein_tor_fit.pdb to my_protein_tor_fit_A_256_I.pdb #
SET OUTPUT_CONTROL = 1 1 1 1 1 SET ATOM_FILES_DIRECTORY = '../templates' READ_TOPOLOGY FILE = '$(LIB)/top_heav.lib' READ_TOPOLOGY TOPOLOGY_MODEL = 3 READ_PARAMETERS FILE = '$(LIB)/par.lib' READ_MODEL FILE = 'my_protein_tor_fit.pdb' SEQUENCE_TO_ALI ADD_SEQUENCE = on, ATOM_FILES = 'my_protein_tor_fit.pdb', ALIGN_CODES = 'my_protein_tor_fit' # Select residue SET SELECTION_SEARCH = 'SEGMENT' SET SELECTION_FROM = 'ALL' PICK_ATOMS SELECTION_SEGMENT = '256:B' '256:B' PICK_ATOMS SELECTION_STATUS = 'INITIALIZE'
MUTATE_MODEL RESIDUE_TYPE = 'ILE'
SEQUENCE_TO_ALI ADD_SEQUENCE = on, ALIGN_CODES = ALIGN_CODES 'my_protein_tor_fit_A_256_I' # Generate molecular topology for the mutant: GENERATE_TOPOLOGY SEQUENCE = 'my_protein_tor_fit_A_256_I'
# Get the model's coordinates from the template, using the alignment TRANSFER_XYZ
# Build the remaining unknown coordinates for the mutant. BUILD_MODEL INITIALIZE_XYZ = off
MAKE_RESTRAINTS RESTRAINT_TYPE = 'stereo' OPTIMIZE OPTIMIZATION_METHOD = 1, MAX_ITERATIONS = 200 OPTIMIZE OPTIMIZATION_METHOD = 3, TEMPERATURE = 300, MAX_ITERATIONS = 25 OPTIMIZE OPTIMIZATION_METHOD = 1, MAX_ITERATIONS = 200 ENERGY
marc
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