Re: [AMBER] question about hydroxyproline and new atom type'OO'

From: David A Case <>
Date: Mon, 8 Jul 2013 16:24:41 -0400

On Mon, Jul 08, 2013, Tianchi Chen wrote:

> I have a question about how to add atom type in leap. I have a
> hydroxyproline parameter file and I want to build a new unit of
> HYP to construct new peptides. on the website it tells me to make
> a new atom type 'OO', which uses many of the older 'OH' atom
> type parameters. The manual show the command "addAtomTypes { {
> type element hybrid } { ... } ... }", and I check the old 'OH'
> hybridization for oxygen is sp3. How do I use this command? like
> "addatomtype {'OO' 'O' 'sp3'} ? I tried several ways it always show
> "ERROR: syntax error". Anyone knows how to use this command and how
> to set up the new atom type?

Two comments:

1. The command is addAtomTypes (note the "s" on the end); LEaP is nowhere
near as smart as the Google (or even the git), and doesn't offer to correct
your spelling. You can see lots of examples of this command in the files
in $AMBERHOME/dat/leap/cmd.

2. The ff12SB library already has HYP as a standard component: maybe this
will suffice.


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Received on Mon Jul 08 2013 - 13:30:04 PDT
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