From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Tue May 08 2007 - 16:46:29 CDT
New to the list and considering to download namd,
first I need information that I found difficult to get
from the web site or archive list:
1) Do Parameters come with namd download or should
they be obtained elsewhere? In particular, how to get
the latest CHARMM (or other) parameters as a starting
2) Where to obtain the list of CHARMM (or other) atoms
to be used?
3) Is any tool provided to build Parameters for any
type of functionalities? Can I use my quantum
mechanical code to make them in the frame of such
tool, if any?
4) How are Partial Charges obtained? Can I use those
provided by my quantum mechanical code?
It should be apparent from my questions that I intend
to use namd for interplay of proteins with organic
compounds of wide variety, thus the code should
perform not for proteins or DNA/RNA only. This is also
why I mentioned CHARMM and nor AMBER.
Huge thanks for directing me to where such information
can be found.
Do You Yahoo!?
Tired of spam? Yahoo! Mail has the best spam protection around
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:44:39 CST