Thanks very much for Prof. Case's explanation. The commands I give to tleap were just common commands, like loadmol2, loadamberparams and saveamberparm and savepdb. For the small molecule, I only load the file and extra parameters and then save the topology and coordinate files, usually I save a copy of pdb file to make sure that there is no error. Why are the nitrogen atoms of small molecules protonated after treated by tleap and the double bonds rearrange? Thanks very much again!
All the best,
qinghua
At 2011-04-13£¬case <case.biomaps.rutgers.edu> wrote:
>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 - 22:30:02 PDT
