[AMBER] Two questions for GAFF

From: Matsuura, Azuma <matsuura.azuma.jp.fujitsu.com>
Date: Wed, 10 May 2017 07:58:16 +0000

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:
            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

            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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Received on Wed May 10 2017 - 01:00:03 PDT
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