first aid

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
point?

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.

francesco pietra

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