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@daviddesancho
daviddesancho / Sdipep.pdb
Created Jul 30, 2019
GMX: clashes after energy minimization / serine2 copies
View Sdipep.pdb
ATOM 1 N SER A 1 -1.435 -2.375 0.469 1.00 0.00 N
ATOM 2 CA SER A 1 0.014 -2.375 0.469 1.00 0.00 C
ATOM 3 C SER A 1 0.537 -0.946 0.469 1.00 0.00 C
ATOM 4 O SER A 1 1.430 -0.610 1.244 1.00 0.00 O
ATOM 5 CB SER A 1 0.566 -3.075 -0.764 1.00 0.00 C
ATOM 6 OG SER A 1 0.205 -2.342 -1.937 1.00 0.00 O
ATOM 7 N SER A 2 -0.022 -0.104 -0.404 1.00 0.00 N
ATOM 8 CA SER A 2 0.388 1.282 -0.502 1.00 0.00 C
ATOM 9 C SER A 2 0.234 1.969 0.847 1.00 0.00 C
ATOM 10 O SER A 2 1.180 2.651 1.237 1.00 0.00 O
@daviddesancho
daviddesancho / md.log
Last active Jul 18, 2019
mdp and log files for free energy simulation in Gromacs
View md.log
Log file opened on Thu Jul 18 09:57:46 2019
Host: villin pid: 32726 rank ID: 0 number of ranks: 1
:-) GROMACS - gmx mdrun, 2018.2 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
Par Bjelkmar Aldert van Buuren Rudi van Drunen Anton Feenstra
Gerrit Groenhof Aleksei Iupinov Christoph Junghans Anca Hamuraru
Vincent Hindriksen Dimitrios Karkoulis Peter Kasson Jiri Kraus
Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl
@daviddesancho
daviddesancho / modeller_test_energy2.py
Created Oct 31, 2016
Test for energy estimation of interfaces within Modeller (https://salilab.org/modeller)
View modeller_test_energy2.py
import modeller
modeller.log.none()
env = modeller.environ()
env.io.hetatm = True
#soft sphere potential
env.edat.dynamic_sphere=False
env.edat.nonbonded_sel_atoms = 2
@daviddesancho
daviddesancho / modeller_test_energy.py
Created Oct 28, 2016
Test for energy estimation of interfaces within Modeller (https://salilab.org/modeller)
View modeller_test_energy.py
import modeller
import Bio
from Bio.PDB import PDBList
# modeller stuff
modeller.log.none()
env = modeller.environ()
env.edat.nonbonded_sel_atoms = 2
# Read customized topology file with phosphoserines (or standard one)
env.libs.topology.read(file='$(LIB)/top_heav.lib')
View stackoverflow24952918tmp.py
import sys, os
import json
import urllib2
import tempfile
import multiprocessing as mp
def worker(url):
""" reading lots of data """
print "# Process %s running on file %s"%(mp.current_process(), url)
raw = json.load(urllib2.urlopen(url))
View stackoverflow24952918.py
import sys
import json
import urllib2
import multiprocessing as mp
def worker(url):
""" reading lots of data """
print "# Process %s running on file %s"%(mp.current_process(), url)
raw = json.load(urllib2.urlopen(url))
data = {}
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