Dear Amber users,
I plan to perform simulations of the protein (preferably with ff14SB ff)
with the modified histidine residue (N-epsilon-phosphohistidine).
I found the necessary parameters at the
http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/pro/phos2_inf.html
database coming from J Mol Model (2006) 12: 281–289, however, as far as I
understand these are suitable for ff99SB force field.
Reading through the list I found a potential solution to this problem
http://archive.ambermd.org/201611/0285.html involving change of the atom
types to the ones in the ff14SB, but this answer, I believe, was in context
of a newer parameter set (J. Chem. Theo. Comput. 8:4405-4412, 2012.), so
called "phos_aa" set.
So here's my question. Is, in your opinion, the procedure of atom type
swapping applicable to the older parameter set, containing parameters for
phosphohistidine or it's rather better to stick with the ff99SB for the
protein residues, or there's potentially another way of solving this
problem.
Many thanks for help,
Jan Ludwiczak
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Received on Thu Dec 28 2017 - 09:00:03 PST
