Re: [AMBER] savePdb in leap

From: case <>
Date: Sat, 6 Mar 2010 10:15:41 -0500

On Fri, Mar 05, 2010, Peter Schmidtke wrote:
> 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.

This will sometimes happen, as LEaP (for some reason) wants to output the
units in order of decreasing size.

To ensure consistency, use ambpdb to construct the pdb files from the
prmtop/inpcrd files.


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Received on Sat Mar 06 2010 - 07:30:02 PST
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