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

From: Jason Swails <jason.swails.gmail.com>
Date: Thu, 28 Aug 2014 21:03:47 -0400

On Thu, Aug 28, 2014 at 7:27 PM, Mohammad Salem <mohammad.alaraby.gmail.com>
wrote:

> 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.
>

‚ÄčThere is actually no FF10SB. FF10 is exactly the same as FF99SB. There
is FF12SB and FF14SB that are incremental improvements to FF99SB.

That said, FF94, FF96, FF99, FF99SB, FF12SB, and FF14SB all use the same
exact charge derivation scheme (the same exact charges, really). So any
charge derivation scheme compatible with one is compatible with all.

You need to derive charges differently for FF03 or FF14IPQ, since those use
a different charge derivation scheme.

HTH,
Jason

-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Aug 28 2014 - 18:30:02 PDT
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