Hai Nguyen hainm
hainm
/ test_sanderapi_log.02052017.BAD.txt
Created
February 5, 2017 06:03
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| amber/test/sanderapi ((no branch, rebasing master)) $ make | |
| make[1]: Entering directory `/net/casegroupp/u1/haichit/amber_git/amber/test/sanderapi' | |
| Creating the bad prmtop test.parm7 | |
| Testing the Fortran API | |
| gfortran -I/home/haichit/amber_git/amber/include -L/home/haichit/amber_git/amber/lib test.F90 -o testf -lsander | |
| Running testf | |
| Checking proper treatment of a bad prmtop | |
| ERROR: Flag "ATOM_NAME" not found in PARM file | |
| PASSED | |
| ============================================================== |
hainm
/ Dockerfile
Last active
November 17, 2016 03:42
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| FROM centos:5 | |
| ENV MINICONDA_URL https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh | |
| ENV MINICONDA_ROOT /root/miniconda3 | |
| RUN yum -y update | |
| RUN yum -y install gcc \ | |
| patch \ | |
| csh \ | |
| flex \ |
hainm
/ pysander_restraint.py
Created
November 14, 2016 20:05
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| import sander | |
| import parmed | |
| options = sander.pme_input() | |
| options.cut = 8.0 | |
| options.ntr = 1 | |
| options.refc = '../ubiquitin/inpcrd' | |
| options.restraintmask = '!:WAT' | |
| options.restraint_wt = 1. |
hainm
/ amber_adaptbx_restraint_amber.sh
Created
November 14, 2016 20:03
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| root_name=../../../files/vAla3/vAla3 | |
| phenix.refine $root_name.pdb\ | |
| $root_name.cif\ | |
| $root_name.mtz\ | |
| topology_file_name=$root_name.prmtop\ | |
| coordinate_file_name=$root_name.rst7\ | |
| use_amber=True \ | |
| wxc_scale=0.025 \ | |
| --overwrite \ | |
| amber.restraint_wt=1.\ |
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| Error compiling Cython file: | |
| ------------------------------------------------------------ | |
| ... | |
| cdef BondArray bondarray, bondarray_h | |
| cdef BondType btype = BondType() | |
| bondarray = self.thisptr.Bonds() | |
| bondarray_h = self.thisptr.BondsH() | |
| bondarray.insert(bondarray.end(), bondarray_h.begin(), bondarray_h.end()) |
hainm
/ run_amber_phenix_test.py
Created
October 13, 2016 18:52
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| import os | |
| import subprocess | |
| import amber_adaptbx | |
| test_path = os.path.dirname(amber_adaptbx.__file__) + '/tests' | |
| # test.fast | |
| command = [ | |
| 'phenix.python', | |
| '-m', |
hainm
/ pysander_pytraj_09132016.py
Created
September 13, 2016 05:46
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| import parmed as pmd | |
| import sander | |
| # make default pme input | |
| inp = sander.pme_input() | |
| parm_file = '../ubiquitin/prmtop' | |
| rst7_file = '../ubiquitin/restrt.save' | |
| parm = pmd.load_file(parm_file, rst7_file) |
hainm
/ parmed_change_name.py
Last active
August 31, 2016 15:39
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| import parmed as pmd | |
| parm = pmd.load_file("old.parm7") | |
| # suppose your H is 1st atom | |
| atom = parm.atoms[0] | |
| # add you stuff here | |
| atom.name = | |
| atom.type = | |
| atom.atomic_number = | |
| atom.charge = | |
| parm.save('new.parm7') |
hainm
/ autorun.js
Last active
June 27, 2016 21:07
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| define([ | |
| 'jquery', | |
| 'base/js/namespace', | |
| 'base/js/events' | |
| ], function ( | |
| $, | |
| IPython, | |
| events | |
| ) { | |
| var run_all_cells = function(){ |
hainm
/ write_data_segmentation_fault.py
Last active
June 16, 2016 16:48
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| import pytraj as pt | |
| from pytraj.core.c_core import Command | |
| from pytraj import CpptrajState | |
| # data is DatasetGridFloat | |
| data = pt.io.read_data('fav8.guv.O.1.ccp4', | |
| options='name MyCcp4')[0] | |
| state = CpptrajState() |
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