AMBER Archive (2008)

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

From: Da-Wei Li (lidawei_at_gmail.com)
Date: Tue Apr 15 2008 - 08:53:06 CDT

The most easy way is to remove the H atoms in the PDB file and let
leap add them.

On Tue, Apr 15, 2008 at 9:43 AM, Cristina Sisu <csds2_at_cam.ac.uk> wrote:
> 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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