AMBER Archive (2008)

Subject: AMBER:

From: uccabke_at_ucl.ac.uk
Date: Thu Apr 17 2008 - 10:02:06 CDT

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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