Dear all,
I am having some troubles in get some (supposedly straightforward) relaxations
results.
I want to relax a benzene molecule in xyz format (this is a test for more
complex results).
I tried both "obminimize" and "obabel --minimize", compiling the source code
and the anaconda3 version.
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 st
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 filenam
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?
Yo
Hi,
obminimize outputs only in pdb format.
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?
Thanks,
Sundar
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Hi Noel,
I tried to minimize ligands using obminimize when using earlier versions of
obminimize after converged the output file will be redirected to a pdb file
format. But when I tried using obminimize of openbabel version 2.4.0 even
after convergence it performs minimization till the completion
> 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 y
Hello Guys
Currently I'm writing my Bachelorthesis and therefor I'm using Openbabel for
some calculations.
Now i have the following problems.
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
cours
he 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
>
&
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
t;
> 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 ----
&g
o 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 y
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
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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Make your web apps faste
> obminimize -ff MMFF94 -sd source.sdf > target.sdf
Indeed, we intentionally do not change the source file. I'd prefer to keep the
original coordinates around in case something strange happened during the
optimization or I wanted to do conformer searching, etc.
Cheers,
-Geoff
-
Try:
obminimize -ff MMFF94 -sd source.sdf > target.sdf
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2013/2/27 Оги Боги
> Hi guys,
>
> I am trying to use obminimize under 64bit windows 7 in order to minimize
> geometry of molecules inside multimolecule sdf file.
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
The problem is that obminimize prints results from minimization procedure in
console but nothing
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
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
--
Is it possible to get the obminimize tool to output anything other than pdb
file format?
--
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> 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
implementati
Hi All,
Could anyone help me to get energy minimal value for more than 2
decimal places, i need atleast 5 decimal places. For example
C O N J U G A T E G R A D I E N T S
STEPS = 2500
STEP n E(n) E(n-1)
1 22.678 22.696
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