Batch minimization of ligands

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Batch minimization of ligands

ishan
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 possible to do batch energy minimization in openbabel? Can anybody suggest me the correct command to do batch minimization?

Thanks and Regards
Ishan
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Re: Batch minimization of ligands

Pranav
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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Re: Batch minimization of ligands

ishan
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] <[hidden email]> wrote:
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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Re: Batch minimization of ligands

Dimitri Maziuk
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 a large number of loosely-coupled tasks, while
High Performance Computing systems tend to focus on tightly coupled
parallel jobs, and as such they must execute within a particular site
with low-latency interconnects.
'''

How tightly are your ligand minimizations coupled?

Dima


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Re: Batch minimization of ligands

Pranav
In reply to this post by ishan
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 if the code you are trying to make parallel has no backward dependency, you can modify the openbabel code and compile it all over again.

Thanks,
Pranav  
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Re: Batch minimization of ligands

David Hall
In reply to this post by ishan
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 <[hidden email]> wrote:
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 possible to do batch energy minimization in openbabel? Can anybody
suggest me the correct command to do batch minimization?

Thanks and Regards
Ishan



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Re: Batch minimization of ligands

Dimitri Maziuk
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 obminimize, too, if one's willing to pay for that. Or
just "for i in *.mol ; do nohup obminimize ... & ; done"

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