Get mol2 file from obminimize

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Get mol2 file from obminimize

Manuel Hechinger
Hello everybody,

I am struggling with the geometry optimization routine "obminimize" within Open Babel. It works perfectly, but I wonder how I can put the resulting structure back into a *.mol2 file, since the result only appears in the command window.

Apart from that, I have two additional questions:

1. Are there already semi-empirical calculation routines for geometry optimization available such as AM1 etc.?
2. Which optimization method should I use, conjugate gradients or steepest descent? Both lead to different results.

Thank you very much for you help and for supplying Open Babel, it is of great help!

Best regards,

Manuel

--
Dipl. Ing. Manuel Hechinger
RWTH Aachen University
AVT - Aachener Verfahrenstechnik
Process Systems Engineering
D- 52056 Aachen

Tel.: +49 241 80-9 70 06
Fax:  +49 241 80-9 23 26

E-Mail:   [hidden email]
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Re: Get mol2 file from obminimize

Geoffrey Hutchison
> I am struggling with the geometry optimization routine "obminimize"  
> within Open Babel. It works perfectly, but I wonder how I can put  
> the resulting structure back into a *.mol2 file, since the result  
> only appears in the command window.

You can redirect output to the terminal, e.g.:

obminimize ... >out.mol2

> 1. Are there already semi-empirical calculation routines for  
> geometry optimization available such as AM1 etc.?

No. I highly doubt we will ever implement quantum mechanics inside  
Open Babel. People have requested some level of molecular mechanics  
for handling conformer searching and 3D coordinate generation (e.g.,  
from SMILES or InChI).

If you're looking for semi-empirical QM, I suggest looking at packages  
like MOPAC2009.

> 2. Which optimization method should I use, conjugate gradients or  
> steepest descent? Both lead to different results.

Ultimately, they should lead to the same minimum geometry, although  
not necessarily with the same number of steps. If your geometry is far  
from a minimum, steepest descent is probably better than conjugate  
gradients. However, the latter is usually faster to converge to a  
minimum.

Cheers,
-Geoff

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Re: Get mol2 file from obminimize

SourceForge.ZAF
In reply to this post by Manuel Hechinger
 But the terminal output geometry from obminimize is always in PDB
format, isn't it?!

> From: Geoffrey Hutchison <...>
> To: Manuel Hechinger <...>

>> I am struggling with the geometry optimization routine "obminimize"
>> within Open Babel. It works perfectly, but I wonder how I can put
>> the resulting structure back into a *.mol2 file, since the result
>> only appears in the command window.
>
> You can redirect output to the terminal, e.g.:
>
> obminimize ... >out.mol2
--
 Zoltan (Zoli) A. Fekete


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Re: Get mol2 file from obminimize

Geoffrey Hutchison

On Oct 12, 2009, at 2:00 AM, [hidden email] wrote:

> But the terminal output geometry from obminimize is always in PDB
> format, isn't it?!

Good point. :-)

I'm happy to add an output format flag to obminimize. If people want  
patches, I'd be glad to send them -- but it otherwise wouldn't be  
incorporated until the next release.

-Geoff

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Re: Get mol2 file from obminimize

Noel O'Boyle
Administrator
2009/10/14 Geoffrey Hutchison <[hidden email]>:

>
> On Oct 12, 2009, at 2:00 AM, [hidden email] wrote:
>
>> But the terminal output geometry from obminimize is always in PDB
>> format, isn't it?!
>
> Good point. :-)
>
> I'm happy to add an output format flag to obminimize. If people want
> patches, I'd be glad to send them -- but it otherwise wouldn't be
> incorporated until the next release.

IMHO, having the output in the same format as the input would be the
best solution.

> -Geoff
>
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Re: Get mol2 file from obminimize

Fredrik Wallner
In reply to this post by Geoffrey Hutchison
Without patches, people should be able to pipe the output through babel such that Geoff's original command would be obminimize ... | babel -ipdb out.mol2

/Fredrik

14 okt 2009 kl. 16.22 skrev Geoffrey Hutchison:


On Oct 12, 2009, at 2:00 AM, [hidden email] wrote:

But the terminal output geometry from obminimize is always in PDB
format, isn't it?!

Good point. :-)

I'm happy to add an output format flag to obminimize. If people want  
patches, I'd be glad to send them -- but it otherwise wouldn't be  
incorporated until the next release.

-Geoff

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Re: Get mol2 file from obminimize

Tim Vandermeersch
On Wed, Oct 14, 2009 at 4:36 PM, Fredrik Wallner <[hidden email]> wrote:
> Without patches, people should be able to pipe the output through babel such
> that Geoff's original command would be obminimize ... | babel -ipdb out.mol2

That's probably the best solution for now. In the future using the
input file format seems the best solution. I'll put it on my todo
list.

Cheers,
Tim

> /Fredrik
> 14 okt 2009 kl. 16.22 skrev Geoffrey Hutchison:
>
> On Oct 12, 2009, at 2:00 AM, [hidden email] wrote:
>
> But the terminal output geometry from obminimize is always in PDB
>
> format, isn't it?!
>
> Good point. :-)
>
> I'm happy to add an output format flag to obminimize. If people want
> patches, I'd be glad to send them -- but it otherwise wouldn't be
> incorporated until the next release.
>
> -Geoff
>
> ------------------------------------------------------------------------------
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>
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>

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