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From: Junmei Wang <junmwang.gmail.com>

Date: Wed, 10 May 2017 08:39:55 -0400

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
*

*>
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

*> http://lists.ambermd.org/mailman/listinfo/amber
*

*>
*

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Received on Wed May 10 2017 - 06:00:05 PDT

Date: Wed, 10 May 2017 08:39:55 -0400

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:

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Received on Wed May 10 2017 - 06:00:05 PDT

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