AMBER Archive (2006)

Subject: AMBER: solvation and His protonation

From: Jardas sucuriba (
Date: Sat Oct 28 2006 - 09:00:44 CDT

Dear amber users,

I have two questions:

a) I solvated my protein with a truncated octahedron of waters, with a total
number of waters around 14000. When I used ambpdb to create the
corresponding pdb file the numbering of residues started again after 9999.
So, I have residues with the same number. I wonder if someone could tell me
if this is a problem just with ambpdb or if the top and crd files are also
“wrong”? Is sander able to interpret each residue as unique when running the

b) My protein is a dimmer and I want to do simulations of the dimmer and of
the monomer. Each monomer has 2 His, one of which is in the interface. In
the dimmer the interface histidine seems to be in the form HID but in the
monomer is completely exposed to the solvent. Does anyone know if it is
correct to still use the HID form in the monomer or if I should use the
protonated form (HIP) instead?

Any help will be highly appreciated.

Thanks a lot

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