Thanks !
Best wishes,
Marek
Dne Sat, 22 Nov 2014 03:35:02 +0100 Carlos Simmerling
<carlos.simmerling.gmail.com> napsal/-a:
> 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
>>
>>
>>
>>
>>
>>
>>
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Received on Sun Nov 23 2014 - 19:00:02 PST
