Hello,
I am going to run some pH-REMD simulations in explicit solvent of an
helical protein.
I understand that CpHMD, and by extension pH-REMD, are parametrised with
ff10 (equivalent to the ff99SB force field used in the original Mongan
paper).
However, since my structure is composed solely of alpha helices, I am
concerned about the tendency of ff99SB (and ff10) to under-stabilise alpha
helices and thus model an unrealistic partial unfolding of the helices.
I understand that ff14SB has some updated torsion terms for Phi and Psi
angles to improve the accuracy of alpha helix simulations.
Could I therefore use ff14SB instead of ff10 to run my CpHMD without
problems or would this require to re-calculate the model compounds pKa,
update the parameters for the ionisable residues, and perhaps other things?
I am not familiar enough with the Amber force fields, so I am not able to
judge how different ff14SB is from ff10, but since the original method was
developed with ff99SB and we now use ff10 for this method, is it a really
big change for the constant pH calculations, to shift to ff14SB?
If only the parameters for the ionisable residues need to be updated, is it
a big task or could it be done easily, would you please be able to give me
some indication about a possible procedure to do this? (sorry, again if
this is a naive question but I am more familiar with Charmm force fields
than with Amber ones).
Many thanks in advance for your help,
Eric
--
Eric Lang
BrisSynBio Postdoctoral Research Associate Modelling
Centre for Computational Chemistry
School of Chemistry - University of Bristol
Bristol BS8 1TS - United Kingdom
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Received on Fri Nov 04 2016 - 08:30:02 PDT
