AMBER Archive (2008)

Subject: Re: AMBER:

From: Da-Wei Li (lidawei_at_gmail.com)
Date: Thu Apr 17 2008 - 10:18:04 CDT

This is because leap does not recognize the H atom due to some name
inconsistent. The most easy way is to remove all H from the PDB file
and let leap add them according to the template. I think you also need
to edit the residue to name to reflect the fact that is is protonated,
such as from LYS to LYP.

dawei

On Thu, Apr 17, 2008 at 11:02 AM, <uccabke_at_ucl.ac.uk> wrote:
> Hi Amber users
>
> I have a pdb file of a protonated protein. When I load this molecule into xleap,
> it adds further H atoms, I do not understand why this happened? (my molecule is
> already containing the necessary number of H atoms for which I only need to
> create inpcrd and prmtop files). But since xleap added further H atom types, it
> complains when I want to create prmtop and inpcrd files such as:
>
> lots of lines like this:
> FATAL: Atom .R<HIE 794>.A<2HB 18> does not have a type.
> FATAL: Atom .R<HIE 794>.A<3HB 19> does not have a type.
> FATAL: Atom .R<HIE 794>.A<OXT 20> does not have a type.
> Failed to generate parameters
> Parameter file was not saved.
>
>
> any help on how to create promtop and inpcrd for an already protonated and ready
> pdb file is much appreciated.
> Regards
> Boutheina
>
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