On 12/27/2016 05:23 PM, David Hall wrote:
> I would iterate over the molecules using pybel, calling localopt on each
> molecule
I would run obminimize under htcondor, but I do have 144-core pool here
and access all the way to OSG if I need it. One could fire up hundreds
of ec2 vms running obminimi
I would iterate over the molecules using pybel, calling localopt on each
molecule
http://open-babel.readthedocs.io/en/latest/UseTheLibrary/Python_PybelAPI.html?highlight=pybel#pybel.Molecule.localopt
On Wed, Dec 21, 2016 at 2:01 PM, ishan wrote:
> Dear All,
>
> I have prepared ligands in chemsk
Hi Ishan,
No, GNU parallel is not something you can use via an API. However, if you
are looking forward to implement it "inherently", you should read more about
parallel computing and multi threading. I have personally tried OpenMP and
OpenACC with openbabel which didn't work out so well. Still i
On 2016-12-25 12:50, ishan wrote:
> Hi Pranav,
>
> Thanks for the reply, that seems to be a nice trick, I will try it. But One
> question still remains whether it is inherently possible in openbabel.
'''
High Throughput Computing is a computing paradigm that focuses on the
efficient execution of
Hi Pranav,
Thanks for the reply, that seems to be a nice trick, I will try it. But One
question still remains whether it is inherently possible in openbabel.
Regards,
Ishan
On Sun, Dec 25, 2016 at 12:32 AM, Pranav [via Open Babel] <
ml-node+s957263n4659636...@n4.nabble.com> wrote:
> Hey Ishan,
Hey Ishan,
You can use "GNU parallel" if you are using Linux/ Unix on a multi-core
processor. You may have to use variables for filenames. Hope you find it
helpful.
Pranav
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Dear All,
I have prepared ligands in chemsketch, now I have to do energy minimization
of the molecules before docking. I want this to be done in batch mode as
there are hundreds of ligands. I have used obminimize -ff MMFF94 -sd
input.mol > output.mol which does only for one molecule.
Is it possib
