A question about the CHARMM force field

From: Hall McDull (jerviedog_at_gmail.com)
Date: Fri May 04 2012 - 07:33:48 CDT

Dear NAMD users,

Recently I read through the par_all22_sugar.inp file, and I found a record
in the BOND section:

HT OT 450.0 0.9572 ! from TIPS3P geometry
HT HT 0.0 1.5139 ! from TIPS3P geometry (for SHAKE

My question is: If the Kb of the bond is zero (the second line above), why
bother to have a record of the this bond in the BONDS section? Does this
has some effect on the simulation?

Moreover, what if the Ktheta of the angle is zero, but I write this angle
out in the ANGLES section? Does this affect the simulation? What about Kchi
in the DIHEDRALS section? For example, I found the line below in the
DIHEDRALS section of the par_all27_prot_na.prm file:

NH2 CT1 C O 0.0000 1 0.00

Thanks for guides or comments.
Best regards,

Jianfeng He

This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:21:57 CST