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


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.