On Thu, Mar 28, 2013 at 6:56 AM, Vlad Cojocaru <
vlad.cojocaru.mpi-muenster.mpg.de> wrote:
> Dear all,
>
> Yet another question on the use of different modified versions of the
> ff99sb force field in AMBER12 ...
> We are currently using ff99SB+pbsc0+ildn+Brueschweiler(NMR-based)
> modifications.
>
> This relies on very old parameter dataset parm99.dat on top of which the
> frcmods of the modifications are added.
> While trying to change the set of ion parameters, we noticed that
> loading an old parameter data set can lead to errors in which the added
> parameters in the frcmod files were not correctly implemented in the
> topology files.
>
When loading parameter (parm.dat or frcmod) files, order matters. The last
parameters loaded overwrite the previous parameters that may have been
there. This is why ff99SB can be implemented as a short frcmod file loaded
on top of parm99.dat (which is, as you point out, an old parameter
database). If this is not true, it's either a subtle detail that you're
missing or a tleap bug that we need to fix. In any case, a reproducible
case would help us diagnose.
Now, when trying to move to using ff10 by loading parm10.dat and all the
> corresponding libraries, I realized that the ff10 is not compatible with
> the ILDN and Brueschweiler modifications. One of the reason for this
> incompatibility is because the Calpha atoms have now a CX atom type ...
>
ff10 and ff99SB are identical for proteins -- I have validated this on a
number of small peptide chains containing each of the standard amino acids.
The main difference is in the nucleic acid FF side, where it has a couple
improvements over ff99.
Since, as you point out, frcmod.ff99SBildn uses the parm99 atom types, you
would have to modify ff99SBildn to operate with parm10.dat. My suggestion
is to target the issues you have with loading frcmods and parm99.dat, since
that will be easier to solve than what you propose below.
>
> My goal is to use the following force field: ff10 + ILDN +
> Best&Hummer(NMR-nased modifications).
> The latter modifications are not even included with AMBER, which is
> rather unfortunate because D.E. Shaw and co-workers has shown that this
> combination leads to the best results in folding simulations among the
> AMBER variants (2012 PLoS One publication)...
>
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Mar 28 2013 - 05:30:03 PDT
