A couple of quesitons...

David Cullinan culli at DELBRUCK.PHARM.SUNYSB.EDU
Fri Oct 13 11:44:04 EST 1995


Greetings, X-PLOR users!

I have a couple of questions that I was hoping the net community might
help me to resolve.
I'm working with double stranded DNA, doing dynamics based on proton NMR
data, if some of my questions are system specific.

1) In the parameter nbonds statement, what values do you use for the 
	eps, cutnb, ctonnb, and ctofnb?  Do you use cdie or rdie?
	shift or switch?  If you have a compelling reason for any of
	these, what is it?

2) When working with a non-standard base (or amino acid, for proteins),
	such as in the case of a chemical modification, do you assign
	the partial charges simply by comparison with similar bonded
	atoms in standard bases/amino acids, or do you use a program
	to calculate the partial charges?  If the latter, which
	program/method do you use to calculate them?  Do they match
	up with the standard xplor partial charges for the unmodified
	bases/amino acids?

OK, so perhaps it is more than a couple of questions, when you break
it down... ;)  Any help and advice would be greatly appreciated.

Thank you!

David Cullinan



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