Dear Junmei,
Thank you very much for your reply.
I'm looking forward to the evaluation of the result, the answer of the first question, and publishing the paper for GAFF2.
All the best
Azuma
-----Original Message-----
From: Junmei Wang [mailto:junmwang.gmail.com]
Sent: Wednesday, May 10, 2017 9:40 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Two questions for GAFF
Dear Azuma,
Let's me first answer your second question. In GAFF2, the parameters for calculating these force constants have been redeveloped to reproduce vibrational frequencies of thousands molecules. In GAFF, those parameters were developed to reproduce the corresponding force constant parameters in biomolecular force fields (such as FF94) and vibrational frequencies of a few model compounds. Molecules involved those parameters can be good test molecules to evaluate the performance of the two force fields. I will post the evaluation results soon.
I will go back to answer your first question a couple days later.
All the best
Junmei
On Wed, May 10, 2017 at 3:58 AM, Matsuura, Azuma < matsuura.azuma.jp.fujitsu.com> wrote:
> Dear All,
>
> I have two questions for GAFF.
>
> The first one is about GAFF1.8: I calculated all force constants of
> GAFF1.8 with respect to angle and compared them to the listed values
> in gaff.dat. Consequently, there were several kcal/mol differences
> between the listed values and the calculated values in the force
> constants with Cl. In the force constants without Cl, however, the
> differences were all within
> 0.1 kcal/mol.
> My calculation is based on Table 4 (Z value of Cl is 1.272) and the
> corrected version of equation (5) in the original paper, that is the
> definition of calculating the angle force constant in GAFF.
> Please tell me why only the angle force constants including Cl are
> badly calculated. Any suggestions would be greatly appreciated.
>
> The following is the example of cl-cc-na:
> cl-cc-na
> Aeq. K
> gaff1.8 121.12 59.42
> my val. 121.12 63.89
>
> The second one is the difference between GAFF1.8 and GAFF2.1 in
> AmberTools17: When investigating the example above, I found the force
> constant of GAFF1.8 and GAFF2.1 was different in spite of the same
> equilibrium bond/angle as follows:
>
> cc-cl cc-na
> Req K Req K
> gaff1.8 1.7354 317.5 1.3802 425.8
> gaff2.1 1.735 190.08 1.380 354.49
>
> cl-cc-na
> Aeq. K
> gaff1.8 121.12 59.42
> gaff2.1 121.120 90.511
>
> Is the calculation method of the force constant in GAFF2.1 is
> different from that in GAFF1.x?
>
> Thank you in advance.
>
> All the best.
> --
> Azuma Matsuura
>
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>
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Received on Wed May 10 2017 - 18:30:02 PDT
