hainm

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

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

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

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.\

hainm

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

import os
import subprocess
import amber_adaptbx

test_path = os.path.dirname(amber_adaptbx.__file__) + '/tests'

# test.fast
command = [
        'phenix.python',
        '-m',

hainm

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

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

define([
    'jquery',
    'base/js/namespace',
    'base/js/events'
], function (
    $,
    IPython,
    events
) {
    var run_all_cells = function(){

hainm

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()