On Tue, Feb 07, 2012, Cihan Aydin wrote:
>
> 1- Strip hydrogens or any other atoms that I want from the prmtop (not
> only waters)?
> 2- Create topologies using any version of leap without adding hydrogens
> or other atoms?
Essentially "no" to both questions. Why do you want to do something like
this? That is, what would you do with such a stripped prmtop file if you
made it? (A prmtop file without hydrogens wouldn't be of much (any?) use
inside the Amber suite of programs.)
....dac
[About the "essentially" part: one could imagine having "united atom"
libraries that don't have hydrogens, e.g. ff03ua. Then hydrogens would not
be added, because they are not needed for that force field. But that just
applies to hydrogens bonded to carbon: hydrogens bonded to N or O would still
be needed.]
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Received on Tue Feb 07 2012 - 17:30:02 PST
