On 29/03/17 13:36, Adriana Sene wrote:
> Hi
Hi,
> I am new here, I am looking for some way to modify one of my ligand. I
> have some cl atoms in the ligand which I wanted to remove and add
> other functional groups. If some one can tell me, how it can be done
> or which tools either free or paid can be used to do that.
>
Let's imagine that you have access to Coot... The details of how to go
about this depend on the nature of your input. Let's also imagine that
you are starting from a SMILES string, then:
Calculate -> Ligand Builder -> File -> Input from SMILES ->
CC(=O)Nc1ccc(O)cc1 -> OK
.. click, click, edit (in a hopefully intuitive manner) [1]
Apply (wait as Coot runs Acedrg for you)... -> molecule appears (and an
mmCIF dictionary is written to the file system (which can be used as
import to Coot/Lidia (just try that with your "paid-for" software)).
You can use File -> Save As... to save in various output formats, press
the SMILES icon to get a 'cut&pasteable' string.
Paul.
[1]
https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/screenshots/coot-lidia-pep.png
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