Hi Marek,
We have not really done much more testing of ff14SB vs ff14SBonlysc for
igb=8. We did use the only school variant in our recent JACS article on
protein folding, so if you haven't seen that you can refer to it for more
discussion, including some discussion of nonpolar solvation.
You're right that at the moment it's hard to use gb for protein-nucleic
acid complexes. A frequent weakness in GB is ion pairing, and these systems
tend to have a high number of phosphate to Arg or Lys. You need to be
careful using gb for that. We do have a nucleic acid variant of GBneck2 in
process and will release it as soon as it's ready.
Carlos
On Nov 21, 2014 9:14 PM, "Marek Maly" <marek.maly.ujep.cz> wrote:
> Hello,
>
> I have 3 questions related to GB simulations in Amber14.
>
>
> 1)
> In Amber14 manual there are these 2 sentences.
>
> page 31
> Currently, it appears that igb=8 may work best with the fully quantum
> mechanics-based dihedral parameters included in ff14SBonlysc. Simulations
> performed in explicit water most likely benefit from the empirical
> corrections included in ff14SB.
>
> page 58
> The combination of the ff14SB force field with igb=8 gives the best
> results for proteins;
>
> -----
> So clear is that igb=8 is actually perhaps the best choice regarding GB
> algorithm for simulations of proteins but it is not so clear if in
> combination with ff14SBonlysc or in combination with ff14SB.
>
> Is it today possible to say something more clear/unambiguous about the
> differences in protein simul. results between [igb=8 + ff14SBonlysc]
> and [igb=8 + ff14SB] ?
>
> 2)
>
> On page 59 there is written:
>
> ff14SB and igb=1 is recommended for nucleic acids (see[131]for an
> evaluation of GB models for DNA).
>
> -----
>
> Naturally one may think about the GB simulations of the mixed
> protein/DNA,RNA systems.
> Which igb value is recommended in that case ?
>
> 3)
> Is it in Amber GB models and especially in mentioned igb=1 and igb=8
> somehow explicitly treated the
> hydrophobic interaction so important e.g. for bigger globular proteins ?
> For the illustration, here is one recent article.
> http://www.ncbi.nlm.nih.gov/pubmed/23479281
>
> Thanks in advance for your comments.
>
> Best wishes,
>
> Marek
>
>
>
>
>
>
>
> --
> Tato zpráva byla vytvořena převratným poštovním klientem Opery:
> http://www.opera.com/mail/
>
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Received on Fri Nov 21 2014 - 19:00:12 PST
