[AMBER] savePdb in leap

From: Peter Schmidtke <pschmidtke.mmb.pcb.ub.es>
Date: Fri, 05 Mar 2010 14:47:34 +0100

Dear Amber users/developers,

I have a question related to leap (ambertools 1.2). When I prepare a system
(solvation etc...) starting with a pdb structure and I dump the results to
the topology & coordinate files (using saveAmberParm) and afterwards in the
same session I dump the coordinates to a pdb file (savePdb), then the order
of atoms in the pdb do not correspond to the order of atoms in the topology
file written just before. Is this known, normal and corrected in
ambertools1.3? Is it fixed by some new bugfix?

I did not try for now, but I saw a statement that ambertools1.3 writes pdb
files using the new pdb standards. Does ptraj etc... write now the elements
in the corresponding element columns or still not?

Thanks in advance.

Peter Schmidtke

PhD Student at the Molecular Modeling and Bioinformatics Group
Dep. Physical Chemistry
Faculty of Pharmacy
University of Barcelona

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Received on Fri Mar 05 2010 - 06:00:15 PST
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