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
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