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
