On 05/31/2012 06:09 AM, Thomas Cheatham wrote:
>> After having "hacked" the topology file of my system,
>> so that to have the protein (which is actually a dimer) and the ligand
>> belonging to the same solute molecule,
> If they were in the same molecule there (i.e. the dimer + ligand all in
> the same molecule) then the periodic imaging would not be able to split
> them assuming you are doing molecule based imaging (which is the default).
> The only way for them to break would be actual disruption of the
> structure.
>
> You can send me off list the prmtop, mdin, short traj, and I can try to
> figure it out... --tom
>
>
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Received on Thu May 31 2012 - 22:30:02 PDT
