Dear Amber users and developers,
I have a problem when I use tleap in order to load the pdb file of a protein containing HIE or HIS residues.
When I load the protein with the loadpdb command, tleap creates a new atom called HD1 for the HIE residue.
However, if I take a look at HIE.lib (or HIS.lib) file, such HD1 atom does not exist for HIE (HIS) residue; indeed, when I create .top and .crd files for such protein, tleap gives an error because this HD1 atom has no an atom type.
Of course I can manually remove this hydrogen atom after I load the pdb, but I do not understand why this problem occurs.
It happened also with other proteins, and not only with the specific one I am focusing on now.
Thanks in advance for your help.
Tommaso
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Received on Fri Feb 26 2016 - 02:30:02 PST
