AMBER Archive (2005)

Subject: Re: AMBER: problems with "protonate"

From: David A. Case (case_at_scripps.edu)
Date: Fri Apr 08 2005 - 10:49:29 CDT

On Thu, Apr 07, 2005, Kenley Barrett wrote:

> I am having some difficulties with the protonate command. I have an
> "abnormal" residue in my protein: a methylated histidine. For some
> reason with this residue (and not with any of the normal residues) the
> protonate command leads to the placement of atoms that are named with
> a "?"

Protonate only knows about ordinary amino acids. If you have a chemical
modification, you will have to modify the PROTON_INFO file (which, as you
will see, is where the "?" are coming from.)

[The "HIC" residue in PROTON_INFO is for a histidine bound to copper, not for
methylated histidine.]

But, are you sure you need protonate at all? In most cases, just letting LEaP
add in missing protons is sufficient.

...good luck....dac

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