I am trying to generate new force field parameters based on quantum mechanical calculation. I used amber manual "parameter development" title for this and I calculated bond-angle-non bond parameters but I am having a hard time obtaning dihedral parameters for aromatics Let's consider about pyrazin. These are gaff2 pyrazin parameters :

ca-ca-nb-ca   2    9.600       180.000          2.000
h4-ca-nb-ca   2    9.600       180.000          2.000
nb-ca-ca-nb   4   14.500       180.000          2.000
h4-ca-ca-nb   4   14.500       180.000          2.000
h4-ca-ca-h4   4   14.500       180.000          2.000

When I scanned "ca-ca-nb-ca" dihedral angels, I found that dihedral bond is breaking at 100 degre and 111 kcal/mol energy. According to manual, if this is an ordinary dihedral ca-ca-nb-ca should have been (111/2=)55,5 kcal/mol V/2 value. But in gaff2 it is just 9.60kcal/mol. There is a huge difference. So, how to obtain such aromatic ring dihedral parameters by using QM calculation? My advisors said: "you should use twist scan not rotational scan" but I am not sure even if "twist-scan" exists and I am not sure "rigid" scan is the true answer. Thank you.

NOTE: Here is the picture.every step is 10 degree.

enter image description here

  • $\begingroup$ Did you find out how to do this? $\endgroup$ – Emerson P L Feb 26 at 15:20

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Browse other questions tagged or ask your own question.