AMBER Archive (2008)

Subject: Re: AMBER: H atom names in Amber

From: uccabke_at_ucl.ac.uk
Date: Thu Apr 17 2008 - 10:49:57 CDT

Hi

My pdb file comes from a result of an MD calculation with Amber.
i have cut out part of if with vmd. To this new part, ie my new pdb file
(created with amber) i want a prmtop and an inpcrd files, what to do?
Amber is adding to it loads of H atoms again when I load it to xleap, and then
complains about new atom types when I try to create prmtop and inpcrd....

Quoting "David A. Case" <case_at_scripps.edu>:

> On Thu, Apr 17, 2008, uccabke_at_ucl.ac.uk wrote:
>>
>> I have a pdb file of a protonated protein. When I load this molecule into
>> xleap, it adds further H atoms
>
> This is probably because the names of the H atoms in your pdb file
> don't mactch those in the LEaP library. Amber uses the IUPAC and "new" PDB
> naming scheme for hydrogens, but many older files still use different names.
>
> You can use the protonate program with the "-k" option to rename your
> H-atoms.
> Look carefully at the small subset of your protein to see what is going on,
> and to see what the protonate program does.
>
> ...good luck...dac
>
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