On Fri, Nov 11, 2011, Qinghua Liao wrote:
>
> After considering of your remind, I separated the ligand into three
> fregments, and loaded into xleap, I almost made it. But I found another
> problem. Since I add two caps of ACE and NME to the small molecule, but
> antechamber didn't treat them as mentioned in tutorial A1, especially the
> atom types.
If you have capping groups on your small molecule (which is using gaff), it
makes sense to treat the capping groups in gaff as well. I'd probably just
have the acetyl group as a part of the first fragment of the ligand, and the
N-methyl as part of the last fragment.
> Another question, the atom type of the carbon in both ACE and NME is CT,
> while it is CX of the carbon in the backbone and CT in some sidechains.I
> simply change CT to CX, will that make some difference?
It probably will not make a difference, but you could test that. I'm not sure
why you think CT is wrong, however.
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Nov 11 2011 - 05:00:03 PST
