Xleap, PDB file format

From: Sophia Kondratova <x357l_at_unb.ca>
Date: Fri 26 Oct 2001 12:00:26 -0300


When I construct a molecule in xleap, it does not give me atom types or
charges for the atoms, and in the tutorials on the website, for example in the
methane tuturial, the tutorial just says to go into the table editor and fill
in the atom types and atom charges. Is that the only way to constuct a
molecule in xleap, where you have to manually type in charges and atom types
in order to construct the appropriate .top and .crd files. Also where are
these values found.

Another question is regarding the pdb file format. What pdb file format does
amber accept, because if I save molecules in pdb format (not proteins but
smaller organic molecules) and I try to open it in xleap, it does not
recognize any atom types and cannot connect the atoms.

Both of these questions are regarding making the appropriate .top and .crd

Any help would be appreciated

Sophia Kondratova
Biochemistry Graduate Student
University of New Brunswick
Fredericton, Canada
Received on Fri Oct 26 2001 - 08:00:26 PDT
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