[AMBER] On combining different force-fields and charge-derivation methods

From: Mohammad Salem <mohammad.alaraby.gmail.com>
Date: Thu, 28 Aug 2014 17:27:29 -0600

Dear All,

I am working on a project involving a protein with an unnatural fragment of the size of 3 amino acids (bonded to the rest of the protein)

I tried using ANTECHAMBER to do my fragment. I got the missing interface parameters from the PARM99 file.
I later did the RED IV run. I just got the charges from that to modify the files that I built with ANTECHAMBER.

Now the simulation will include parameters as follows: For the fragment, it got its atom types from GAFF (as made by antechamber) and the charges from RED. The missing parameters I got from PARM99 and the rest of protein is dealt with regularly with, say, FF10SB.

I am a newbie to dynamics, so I need an expert advice. Do you think this is a reasonable cocktail? :)


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Received on Thu Aug 28 2014 - 16:30:02 PDT
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