AMBER Archive (2000)

Subject: Re: how to get unusual topology in leap

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Thu Mar 23 2000 - 13:25:00 CST

        I need to prepare 'fake' topology for my system which would include,
        say, only backbone atoms. ...
        (1) I loaded pdb file which only had backbone atoms but leap
        automatically adds whole residues according to library templates. Is
        there a way to prevent this and yet be able to write out 'syntactically'
        valid topology file?

- make a template of a new residue that is only backbone
- strip non-backbone atoms from pdb
- change res names in pdb to name of new residue
- loadpdb

What program uses the prmtop? As a side issue, if it only uses
the connectivity info, perhaps using pdb format with CONECT records
would be more general.

        Is there
        a way to select (and delete) atoms by atom types in a more general way
        than typing each subunit explicitly using leap's dot notation
        (unit.ALA.3 etc.)?

No.. it might not be hard to add, however.

Bill Ross