On Wed, 13 Oct 2004 13:14:21 +0200
Marc Gasser <> 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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