AMBER Archive (2001)

Subject: Re: Help with Leap!

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Mon Jul 09 2001 - 19:34:52 CDT

        I use the xLEAP program to read in a PDB file of a RNA molecule (with
        some non-standard stuffs in it). However, it added automatically a bunch
        of additional atoms that I do not want. SO, I was just wondering if
        there is anyway that I can turn this automatic feature of the LEAP
        program OFF? Thank you for your help!

If you want to do non-standard things, you need to use
non-standard residue names. Assuming you want to use
leap to generate a prmtop, these new residues will need
to be defined with atom types and charges etc, like
in the tutorials. It should be relatively easy to do
this, mapping from the standard residues.

Bill Ross