Dear Zoran
Sorry here is the sqm output file
here 1 of H from ring Oxygen moved to Phosphate Oxygen.
please suggest
thank you
On Sat, Jun 22, 2019 at 4:19 PM <zmatovic.kg.ac.rs> wrote:
> "I am trying to generate parameters for my ligand when I submit the
> following command antechamber -i BG6_noH.mol2 -fi mol2 -o BG6_amber.mol2
> -fo mol2 -c bcc -pf yes -nc -2 -at gaff2 -j 4
>
> I get the structure which is different from the submitted one.
> I wonder which structure I need to use in tleap because the BG6_amber.mol2
> is not right I am a little bit confused why it has changed and for which it
> has generated parameters either for BG6_noH.mol2 or BG6_amber.mol2."
>
> I do not see different structures instead they are exactly the same with
> just new charges according to the method chosen. Please be more explicit in
> defining the problem.
>
> Zoran
>
>
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Received on Sat Jun 22 2019 - 09:00:02 PDT
