Re: [Open Babel] obminimize outputs only in pdb (multimolecule pdb)

[Sundar]

Hi Geoff,

When I tried to convert a multimolecule pdb file (output from obminimize)
to an sdf file, only the first molecule was converted.
I wrote my own script to split the file into multiple pdbs and put them
together as single sdf using obabel.
But any solution using obabel to that in single step i.e. converting
multimolecular pdb to sdf?

Thanks,
Sundar

On Thu, Oct 19, 2017 at 8:01 PM, Sundar Jubilant 
wrote:

> Thanks. I will try that.
>
> Sundar Thangapandian
>
> > On Oct 19, 2017, at 6:40 PM, Geoffrey Hutchison <
> geoff.hutchi...@gmail.com> wrote:
> >
> > The obminimize program does not have all the features of the obabel
> command. You can naturally convert a PDB file to SDF:
> >
> > obabel file.pdb -O file.sdf
> >
> >> I tried -osdf filename.sdf and it didn't work. How can I get it in sdf
> format?
> >> Or how can I convert multimolecule pdb file to an sdf file?
> >
> > You can also use the --minimize flag with obabel to minimize molecules.
> > http://open-babel.readthedocs.io/en/latest/Command-line_
> tools/babel.html?highlight=minimize#forcefield-energy-and-minimization
> >
> > Hope that helps,
> > -Geoff
>
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Re: [Open Babel] obminimize outputs only in pdb (multimolecule pdb)

[Sundar Jubilant]

Thanks. I will try that.

Sundar Thangapandian

> On Oct 19, 2017, at 6:40 PM, Geoffrey Hutchison  
> wrote:
> 
> The obminimize program does not have all the features of the obabel command. 
> You can naturally convert a PDB file to SDF:
> 
> obabel file.pdb -O file.sdf
> 
>> I tried -osdf filename.sdf and it didn't work. How can I get it in sdf 
>> format?
>> Or how can I convert multimolecule pdb file to an sdf file?
> 
> You can also use the --minimize flag with obabel to minimize molecules.
> http://open-babel.readthedocs.io/en/latest/Command-line_tools/babel.html?highlight=minimize#forcefield-energy-and-minimization
> 
> Hope that helps,
> -Geoff

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Re: [Open Babel] obminimize outputs only in pdb (multimolecule pdb)

[Geoffrey Hutchison]

The obminimize program does not have all the features of the obabel command. 
You can naturally convert a PDB file to SDF:

obabel file.pdb -O file.sdf

> I tried -osdf filename.sdf and it didn't work. How can I get it in sdf format?
> Or how can I convert multimolecule pdb file to an sdf file?

You can also use the --minimize flag with obabel to minimize molecules.
http://open-babel.readthedocs.io/en/latest/Command-line_tools/babel.html?highlight=minimize#forcefield-energy-and-minimization

Hope that helps,
-Geoff
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Re: [Open Babel] obminimize

[Geoffrey Hutchison]

> If i use: obminimize [-ff forcield] [-algorithm]  to calculate the 
> minimized energy of a given ligand a don't always get the same results. (of 
> course I only compare results with the same ligande, same forcefield and same 
> algorithm with each other)


I'm not quite sure I understand what you're doing. For many molecules, 
different starting geometries (even subtly different) can lead to different 
conformations - and thus different energies.

> But for most of the ligands the results are not reproducible. It also depends 
> on the ligand which forcefields deliver reproducible results.

Can you give us an example molecule and/or case of what you're trying to do?

Thanks very much,
-Geoff

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Re: [Open Babel] obminimize

[Оги Боги]

Thank you guys for your answer. I tried what you said but the output is not a 
sdf file. How to format it in order to obtain normal sdf file?

alchemist

 
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Re: [Open Babel] obminimize

[Оги Боги]

  How stupid I am!   Thanks Fredrik, that fix the problem.
So thanks anyone for helping me.

alchemist








  Оригинално писмо 

От: Fredrik Wallner fred...@wallner.nu

Относно: Re: [Open Babel] obminimize

До: Оги Боги  

Изпратено на: Четвъртък, 2013, Февруари 28 14:59:46 EET



 
 
  Hi,
   
   

   
   
   You should have two dashes before ff, that is

obabel orig.sdf -O
 result.sdf --minimize --sd --ff MMFF94 
   
   

 
   
   
   /Fredrik
   
   
   


 
 28 feb 2013 kl. 13:25 skrev Оги Боги 
  alchemist...@abv.bg :
 
 
 
  
   Thank you, Chris
  
It seems that it works fine now. But I would like to change force field. Ho to 
do that? I tried
  

  

   obabel orig.sdf -O
 result.sdf --minimize --sd -ff MMFF94 
  

  
but openbabel says:
  

   Cannot read input format  for file MMFF94 
  

  
Could anyone tell me how to change force field?
  
alchemist
  

  

  

  
  Оригинално писмо  
  
От: Chris Morley 
   c.mor...@gaseq.co.uk  
  
Относно: Re: [Open Babel] obminimize 
  
До: 
   openbabel-discuss@lists.sourceforge.net  
  
Изпратено на: Четвъртък, 2013, Февруари 28 12:07:12 EET 
  

  
On 28/02/2013 07:48, Оги Боги wrote:
  
  Thank you guys for your answer. I tried what you said but the output is
  
  not a sdf file. How to format it in order to obtain normal sdf file?
  
 
  
 An alternative way of accessing the same functionality is to use the 
  
 --minimize op with obabel, which provides more flexibility in the input 
  
 and output. So, for instance,
  
 
  
 obabel orig.sdf -O result.sdf --minimize -f1 -l2
  
 
  
 will optimize the first two molecules in orig.sdf and output to 
  
 result.sdf. Type obabel -L minimize for more details.
  
 
  
 Chris
  
 
  
 
  
 
  
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Re: [Open Babel] obminimize

[Maciek Wójcikowski]

Try:
obminimize -ff MMFF94 -sd source.sdf  target.sdf


Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl


2013/2/27 Оги Боги alchemist...@abv.bg

  Hi guys,

 I am trying to use obminimize under 64bit windows 7 in order to minimize
 geometry of molecules inside multimolecule sdf file. I'm using the
 following command:

 obminimize -ff MMFF94 -sd path-to-sdf

 The problem is that obminimize prints results from minimization procedure
 in console but nothing happens with atom coordinates in sdf file. Is that
 normal or I've made some mistake?





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Re: [Open Babel] obminimize

[Geoffrey Hutchison]

On Feb 18, 2011, at 11:43 AM, christophersw...@btconnect.com wrote:

 Is it possible to get the obminimize tool to output anything other than pdb 
 file format?

Yes. Supply a '-o[ext]' flag. This works with v2.2 or later. Come to think of 
it, *you* asked for the feature! :-)

Cheers,
-Geoff
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Re: [Open Babel] obminimize

[christophersw...@btconnect.com]

Great after a few attempts I see what my problem was:-

If I try the sort of construction used for other babel commands

ChrisMacbookPro:~ swain$ /usr/local/bin/obminimize -ff -ff Ghemical -cg -n 2500 
-c 1.0E-5 -cut -rvdw6.0 -rele 10.0 -pf 10 '/Users/swain/Desktop/output.sdf' 
-osdf  '/Users/swain/Desktop/obmin2'
/usr/local/bin/obminimize: cannot read input/output format!
ChrisMacbookPro:~ swain$ 

or

ChrisMacbookPro:~ swain$ /usr/local/bin/obminimize -ff -ff Ghemical -cg -n 2500 
-c 1.0E-5 -cut -rvdw6.0 -rele 10.0 -pf 10 -isdf 
'/Users/swain/Desktop/output.sdf' -osdf  '/Users/swain/Desktop/obmin2'

No file is written


But using

ChrisMacbookPro:~ swain$ /usr/local/bin/obminimize -ff -ff Ghemical -cg -n 2500 
-c 1.0E-5 -cut -rvdw6.0 -rele 10.0 -pf 10 -osdf 
'/Users/swain/Desktop/output.sdf'   '/Users/swain/Desktop/obmin2'


It works!!

Thanks

Chris




On 18 Feb 2011, at 16:48, Geoffrey Hutchison wrote:

 
 On Feb 18, 2011, at 11:43 AM, christophersw...@btconnect.com wrote:
 
 Is it possible to get the obminimize tool to output anything other than pdb 
 file format?
 
 Yes. Supply a '-o[ext]' flag. This works with v2.2 or later. Come to think of 
 it, *you* asked for the feature! :-)
 
 Cheers,
 -Geoff


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Re: [Open Babel] Obminimize

[Geoffrey Hutchison]

  Could anyone help me to get energy minimal value for more than 2 
 decimal places, i need atleast 5 decimal places. For example 

I highly doubt the molecular mechanics energies have more than 2-3 decimal 
places of accuracy in either the model or implementation. (Yes, the 
implementation performs all calculations with double floating point math, but 
we can't easily validate our implementation to that accuracy.)

Why do you need 5 decimal places? Depending on the force field, we're talking 
about kJ/mol or kcal/mol -- in both cases, that's a vanishingly small energy 
difference.

Best regards,
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