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

From: Karl N. Kirschner <>
Date: Tue, 9 Jul 2013 09:18:29 +0200 (CEST)

Hello Tianchi,

  If you wish to have complete control and understanding of the atom types and parameters for your new residue, you can create and edit (using a text editor, e.g. vi) several files to do this. This will require a good understanding of Amber's force-field files and their format, which I think is always a good idea. Here is the general outline of those files:

1. leaprc file - contains the basic atom type definition and a reference to the created frcmod file (see next point).
2. frcmod file - contains the parameters that are not present in your specified standard force field (e.g. parm99SB).
3. residue file - this can be in a prep or mol2 format.

  Once created you can reference your the leaprc and residue files in a leap input file, and use the more traditional leap commands normally. The question then comes to how trustworthy are your parameters, both bonded and nonbonded, involving your new atom type.


----- Original Message -----
From: "Tianchi Chen" <>
Sent: Monday, July 8, 2013 9:47:51 PM
Subject: [AMBER] question about hydroxyproline and new atom type'OO'

   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?

Tianchi Chen
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Received on Tue Jul 09 2013 - 00:30:02 PDT
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