Re: [AMBER] Phosphoryated amino acids

From: David A Case <>
Date: Thu, 17 Nov 2016 08:39:19 -0500

On Thu, Nov 17, 2016, Eiros Zamora, Juan wrote:

> May I also ask if the ff14SB compatible parameters are available anywhere?

To summarize the situation:

The family of Amber force fields from ff94 -> ff99SB -> ff14SB all use the
same charge model and vdW parameters. This model is also used for the
"phosaa10" parameters, so in this sense the phosphorylated parameters should
be compatible with any of the three protein force fields listed above.

In going from ff99SB to ff14SB, some atom types were changed, leading to new
torsional potentials for both backbones and sidechains. The new backbone
torsions are very likely to be still OK when the side chain is phosphorylated,
and my guess is that the same statement is true for sidechain torsions.
To the extent that this is true, you would want to change the atom types for
CA and CB in phos_amino94.lib to match the types in amino12.lib.

Of course, this is not equivalent to re-fitting the side chain torsions
for the phosphorylated amino acids. But, in my view, using ff14SB
+ phosaa10 (with modified atom types) is almost certainly a better
combination that using ff99SB + un-modified phosaa10: in the original
phosaa10 work, we assumed that the torsion potentials could transfered from
serine to phosphoserine (etc.) You would be making the same assumption
for ff14SB, but transferring the much-improved torsional profiles that are
present in ff14SB. And, of course, all the non-phosphorylated parts of
the protein will be better described with the new force field.

...hope this helps....[Carlos may wish to weigh in here as well]....dac

AMBER mailing list
Received on Thu Nov 17 2016 - 06:00:03 PST
Custom Search