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@ajasja
ajasja / log
Created August 6, 2020 06:22
pdb4amber -i ../../models/w2c_24A_xtal.pdb -o out/w2c_24A_xtal__00_raw_00_clean.pdb --dry --strip @/H --logfile stdout
==================================================
Summary of pdb4amber for: ../../models/w2c_24A_xtal.pdb
===================================================
----------Chains
The following (original) chains have been found:
A
B
@ajasja
ajasja / prepare_amber.py
Last active August 2, 2020 06:59
def run_command(cmd):
"""Runs command, writes to stdout, raises exception on error"""
print(cmd)
#!{cmd}
exit_code = os.system(cmd)
assert exit_code == 0, 'Error running command'
def prepare_system(input_pdb, out_base, suffix='00_raw', skip_existing=True):
assert os.path.exists(input_pdb), f'{input_pdb} does not exists!'
final_name = f'{out_base}__{suffix}.top'
@ajasja
ajasja / box.py
Created July 29, 2020 20:54
from simtk.openmm import *
from simtk.openmm.app import *
from simtk.unit import *
from pdbfixer import PDBFixer
nm = nanometer
fixer = PDBFixer(filename='test/1wa3_BA-05_modl.pdb')
fixer.findMissingResidues()
fixer.findNonstandardResidues()
#fixer.replaceNonstandardResidues()
@ajasja
ajasja / script.py
Created July 29, 2020 01:06
# This script was generated by OpenMM-Setup on 2020-07-28.
from simtk.openmm import *
from simtk.openmm.app import *
from simtk.unit import *
#try:
# platform = Platform.getPlatformByName('OpenCL')
# platformProperties = {'Precision': 'mixed'}
#except:
@ajasja
ajasja / Sym_tree
Created July 16, 2020 03:11
VRT(1342)----=j10=--->VRT_-2_0_0(1343)
|----#j11#--->VRT_-1_0_0(1358)
| |----j1=4----->57:Sub1A(1-149)
| |----=j12=--->VRT_-1_10_0(1368)
| |----=j13=--->VRT_-1_11_0(1369)
| |----=j14=--->VRT_-1_12_0(1370)
| |----=j15=--->VRT_-1_13_0(1371)----j2=4---->206:Sub2A(150-298)
| |----=j16=--->VRT_-1_14_0(1372)----j3=4---->355:Sub3A(299-447)
| |----=j17=--->VRT_-1_1_0(1359)
| |----=j18=--->VRT_-1_2_0(1360)
@ajasja
ajasja / Sym_tree
Created July 16, 2020 03:11
VRT(1342)----=j10=--->VRT_-2_0_0(1343)
|----#j11#--->VRT_-1_0_0(1358)
| |----j1=4----->57:Sub1A(1-149)
| |----=j12=--->VRT_-1_10_0(1368)
| |----=j13=--->VRT_-1_11_0(1369)
| |----=j14=--->VRT_-1_12_0(1370)
| |----=j15=--->VRT_-1_13_0(1371)----j2=4---->206:Sub2A(150-298)
| |----=j16=--->VRT_-1_14_0(1372)----j3=4---->355:Sub3A(299-447)
| |----=j17=--->VRT_-1_1_0(1359)
| |----=j18=--->VRT_-1_2_0(1360)
@ajasja
ajasja / Sym_tree
Created July 16, 2020 03:11
VRT(1342)----=j10=--->VRT_-2_0_0(1343)
|----#j11#--->VRT_-1_0_0(1358)
| |----j1=4----->57:Sub1A(1-149)
| |----=j12=--->VRT_-1_10_0(1368)
| |----=j13=--->VRT_-1_11_0(1369)
| |----=j14=--->VRT_-1_12_0(1370)
| |----=j15=--->VRT_-1_13_0(1371)----j2=4---->206:Sub2A(150-298)
| |----=j16=--->VRT_-1_14_0(1372)----j3=4---->355:Sub3A(299-447)
| |----=j17=--->VRT_-1_1_0(1359)
| |----=j18=--->VRT_-1_2_0(1360)
@ajasja
ajasja / Sym_tree
Created July 16, 2020 03:11
VRT(1342)----=j10=--->VRT_-2_0_0(1343)
|----#j11#--->VRT_-1_0_0(1358)
| |----j1=4----->57:Sub1A(1-149)
| |----=j12=--->VRT_-1_10_0(1368)
| |----=j13=--->VRT_-1_11_0(1369)
| |----=j14=--->VRT_-1_12_0(1370)
| |----=j15=--->VRT_-1_13_0(1371)----j2=4---->206:Sub2A(150-298)
| |----=j16=--->VRT_-1_14_0(1372)----j3=4---->355:Sub3A(299-447)
| |----=j17=--->VRT_-1_1_0(1359)
| |----=j18=--->VRT_-1_2_0(1360)
@ajasja
ajasja / labels
Created July 16, 2020 00:40
REMARK PDBinfo-LABEL: 1 sym_surf
REMARK PDBinfo-LABEL: 2 sym_core
REMARK PDBinfo-LABEL: 3 full_bbi sym_surf
REMARK PDBinfo-LABEL: 4 full_bbi sym_surf
REMARK PDBinfo-LABEL: 5 sym_core
REMARK PDBinfo-LABEL: 6 full_bbi sym_core
REMARK PDBinfo-LABEL: 7 full_bbi sym_core
REMARK PDBinfo-LABEL: 8 sym_surf
REMARK PDBinfo-LABEL: 9 sym_core
REMARK PDBinfo-LABEL: 10 full_bbi sym_core
@ajasja
ajasja / pyrosetta_example
Created January 23, 2019 00:15
#Pyrosetta unsupported BuriedUnsatHbonds2 InterfaceHoles CavityVolume
pack_protocol = """<ROSETTASCRIPTS>
<SCOREFXNS>
### add Nov15 energy function with coordinate constraints
<ScoreFunction name="NOV15" weights="beta" >
<Reweight scoretype="coordinate_constraint" weight="1" />
</ScoreFunction>
<ScoreFunction name="VDW" weights="empty" >
<Reweight scoretype="fa_atr" weight="1.0" />
</ScoreFunction>