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

From: Tianchi Chen <>
Date: Tue, 9 Jul 2013 12:46:20 -0400

thank you David, I solved it. and I should use " instead of ' , also I missed "s", but I didn't find HYP as one of the standard unit in ff12SB.
On Jul 8, 2013, at 4:24 PM, David A Case <> wrote:

> 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.
> ...dac
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Received on Tue Jul 09 2013 - 10:00:04 PDT
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