Thank you !
BTW that difference in c3-c3 force constant GAFF vs GAFF2 is really big
300.9 vs 232.52 I would say. To be frank I am a bit confused with such a
big change moreover in such basic/common atomtype bonding term.
This indicates that methodology and/or set of molecular fragments which
were used for fitting in GAFF2 case had to be quite different from
methodology or mol. fragments used in GAFF case.
I am also a bit confused with the fact that the same term in actually
recommended protein force field ff14SB has still force constant close to
old GAFF value:
CT-CT 310.0 1.526 JCC,7,(1986),230; AA, SUGARS
So old GAFF seems to me to be a more compatible with ff14SB from this
point of view than with the new GAFF2, which is a bit strange or not ?
BTW the same trend holds if we compare here GAFF/GAFF2 with LIPID14 ff.
cA-cA 303.1 1.5350 Lipid11 v1.0 (GAFF c3-c3)
cD-cD 303.1 1.5350 Lipid14 v2.0 (GAFF c3-c3)
again we are much closer here to GAFF values.
The same trend holds for vdW terms:
GAFF
c3 1.9080 0.1094 OPLS
GAFF2
c3 1.9069 0.1078
FF14SB (parm10)
CT 1.9080 0.1094 Spellmeyer
LIPID14
cA 1.9080 0.1094 OPLS
cD 1.9080 0.1094 OPLS
So it seems that if one is going to simulate some heterogenous system
(e.g. protein + drug) it should be more suitable to use still old GAFF
(not the new GAFF2) as GAFF is clearly more compatible
with bio-force-fields than GAFF2 or am I wrong here ?
Best wishes,
Marek
Dne Tue, 24 Jan 2017 19:44:34 +0100 David Case <david.case.rutgers.edu>
napsal/-a:
> On Tue, Jan 24, 2017, Marek Maly wrote:
>>
>> I have technical question regarding QM methods used in GAFF2
>> development.
>
> cc-ing to Junmei Wang, who doesn't always follow the mailing list. Note
> that
> you may need to wait for the paper on GAFF2 to be published...
>
> ...dac
>
>>
>> In Amber16 manual, page 286, there is written:
>>
>> "We have performed B3LYP/6-31G* optimization for 15 thousands
>> marketed or
>> experimental ..."
>>
>>
>> So B3LYP/6-31G* is here QM method used to obtain optimized molecular
>> structures (low energy
>> conformations) from which equilibrium geometrical terms (eq. bond
>> lengths,
>> eq. angles) were obtained
>> and so in some cases old GAFF values were updated.
>>
>>
>> But in GAFF2, comparing to GAFF, changed clearly also some force
>> constants.
>> As an example I can mention c3-c3 bond:
>>
>>
>> In GAFF
>> c3-c3 300.9 1.5375 SOURCE1_SOURCE5 88072 0.0058
>>
>> In GAFF2
>> c3-c3 232.52 1.538 SOURCE1_SOURCE5 88072 0.0058
>>
>>
>> My question is, which QM methodology was used to derive (perhaps using
>> paramfit ?) new GAFF2 bond, angle or dihedral force constants ?
>>
>> I assume, that since here we need just to calculate for each
>> conformation
>> only it's
>> energy (no optimization) and since we also need to obtain reliable
>> force
>> constants (hence we need accurate QM energies) some more accurate method
>> was probably used like MP2/6-31G** , MP3/6-31G** etc. to derive QM
>> energies. Am I right ?
>>
>> So thank you in advance for QM methodology specification used in GAFF2
>> for
>> force constants
>> derivation.
>>
>> Best wishes,
>>
>> Marek
>>
>
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Received on Tue Jan 24 2017 - 17:30:02 PST
