[AMBER] forcefield modifications

From: Knips, Alexander <alexander.knips.ph.tum.de>
Date: Mon, 16 Apr 2012 16:23:25 +0000

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,
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Received on Mon Apr 16 2012 - 09:30:05 PDT
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