On Wed, Apr 13, 2011, fancy2012 wrote:
>
> Yesterday, when I prepared its prmtop and inpcrd files in tleap, two
> nitrogen atoms were protonated and the double bonds rearranged. So how
> should I avoid this protonation and rearrangement of double bond? Thanks
> very much!
??? We would need to know at least *some* information about what commands
you gave to tleap, etc. Leap only adds atoms to a unit if they are present in
the library file but missing in the input pdb (or similar) file. Maybe that
will help.
Concerning double bonds, start here:
http://archive.ambermd.org/201104/0201.html
...dac
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Received on Tue Apr 12 2011 - 20:30:04 PDT
