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 - 00:30:02 PDT
