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

From: Mohammad Salem <mohammad.alaraby.gmail.com>
Date: Thu, 28 Aug 2014 22:13:35 -0600

> ‚ÄčThere is actually no FF10SB.

yup! I actually used FF12SB! Thanks!

> So any
> charge derivation scheme compatible with one is compatible with all.

Sounds good! Thanks!
On Aug 28, 2014, at 7:03 PM, Jason Swails <jason.swails.gmail.com> wrote:

> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
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Received on Thu Aug 28 2014 - 21:30:02 PDT
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