daviddesancho

Copyright 2020 Robert T. McGibbon

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE O

daviddesancho

daviddesancho

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

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

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

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')

daviddesancho

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))

daviddesancho

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 = {}