[AMBER] Can ff14SB be used instead of ff10 for CpHMD simulations?

From: Eric Lang <eric.lang.bristol.ac.uk>
Date: Fri, 4 Nov 2016 15:08:55 +0000


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

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 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
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