Dear all,
I am using Ambertools in typical fashion to generate top and crd files for a molecule.
This is what I have noticed:
In generating the top file for an isolated molecule, same molecule plus 2A TIP3P box and same molecule plus 10A TIP3P box the number of atoms and bonds increase as expected. The number of angles and dihedrals remain at the level of the isolated atom.
Is this behaviour intented?
I did this with the Tp example and used exactly the commands as described in the Ambertools manual.
Any comments are highly appreciated,
Markus
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Received on Sat Mar 26 2011 - 11:00:03 PDT
