Hi guys,
I am actually still confused on how the forcefield modifications in AMBER work specifically.
In my case I have a nucleic structure and changed a specific residue. Lets call it YYY.
For this residue I implemented he specific forcefield modifications according to a paper.
For example an angle parameter like C -N -C is changed in my YYY.frcmod file. Now I still don't understand whether the YYY.frmod changed the angle parameter for all residues or just for the previously unknown YYY residue.
Besides, I also implemented a YYY.prepin
I tried to use rdparm to compare supposedly unchanged residues but that worked out to be really hard as he order of the parameters is completely different.
I would appreciate your help.
With best regards,
Alexander
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Received on Wed Apr 11 2012 - 05:30:06 PDT
