Re: how to get unusual topology in leap

From: Bill Ross <>
Date: Thu 23 Mar 2000 11:25:00 -0800 (PST)

        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
Received on Thu Mar 23 2000 - 11:25:00 PST
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