AMBER Archive (2008)

Subject: AMBER: loading pdb in leap to create parameter files

From: Cristina Sisu (csds2_at_cam.ac.uk)
Date: Tue Apr 15 2008 - 08:43:57 CDT

Dear AMBERs,

I am new in working with Amber. I am using Amber 9, and I got stuck
quite at the beginning of creating the parameter files .prmtop and
.inpcrd. The story is like this:
     I've downloaded a pdb from the protein databank (NMR sturcture).
I've edited the file to save only one model for the protein. I've loaded
the file into leap for creating the parameter files. When I load it, it
automatically ads H atoms to the 3 HIS residues, on the N, charging
therefore my molecule. However at the end of this process I get the
following massage:
"""
> Created a new atom named: HD1 within residue: .R<HIE 3>
> Created a new atom named: HD1 within residue: .R<HIE 86>
> Created a new atom named: HD1 within residue: .R<HIE 100>
> total atoms in file: 2069
> Leap added 3 missing atoms according to residue templates:
> 3 H / lone pairs
> The file contained 3 atoms not in residue templates
> Since added/missing = extra, there is a high probability
> of atoms with 'incorrect' names; you may want to
> use addPdbAtomMap to map these names, or change in file
"""
First time, I've ignored their warning and I tried to go on saving my
parameter files. However I got the error:
"""
> FATAL: Atom .R<HIE 3>.A<HD1 18> does not have a type.
> FATAL: Atom .R<HIE 86>.A<HD1 18> does not have a type.
> FATAL: Atom .R<HIE 100>.A<HD1 18> does not have a type.
> Failed to generate parameters
> Parameter file was not saved.
"""

I've tried then to use the AddPdbAtomMap option trying to indicate that
I want the HD1 atoms to be regarded as HE2 (already in the HIS map file,
Hydrogen atoms)

> addPdbAtomMap {{HE2 HD1}}

Then I've looked at the description for His in the aminoacid database of
Amber. It has only 17 described atoms, and obviously the new H on the N
is not present.
I've looked for an answer in the manual, on the FAQ and in the mail
archive, but I found no answer. Can you please help me figure out how
          - to define the type of the new atom create?
          or
          - to make Amber do not add H on my protein?
          or
          - anyother way to solve this problem?

Thanks,

Cristina
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