On Sun, Mar 17, 2024, SUBHASMITA MAHAPATRA MAHAPATRA via AMBER wrote:
>
>I have been generating .prmtop and .inpcrd files using the PDB:3AYD. It has
>a modified glycan molecule as there is a bond between A2G and NPO. I did
>antechamber for the whole ligand molecule. But, I faced the following error.
>Warning: This molecule has no hydrogens nor halogens.
This is almost certainly wrong: antechamber needs input where the hydrogens
are already present.
Try getting a recent version of AmberTools (or just of cpptraj), and look
at the "prepareforleap" action. This is generally the easiest way to handle
glycans: it uses the glycam force field rather than gaff, but that is
probably an advantage. I think it avoids the need for you to add the
hydrogens that would be needed by antechamber.
....good luck...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Mar 17 2024 - 19:30:02 PDT
