Thank you Karl for your suggestions and I have already this problem.
On Jul 9, 2013, at 3:18 AM, Karl N. Kirschner <kkirsch.scai.fraunhofer.de> wrote:
> 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.
>
> Cheers,
> Karl
>
> ----- Original Message -----
> From: "Tianchi Chen" <tchen11.ncsu.edu>
> To: amber.ambermd.org
> Sent: Monday, July 8, 2013 9:47:51 PM
> Subject: [AMBER] question about hydroxyproline and new atom type'OO'
>
> Hello:
> 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?
>
> Thanks.
> Tianchi Chen
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Received on Tue Jul 09 2013 - 10:00:04 PDT
