From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue May 08 2007 - 17:06:43 CDT
Hi Francesco,
the answers to your first couple of questions can be obtained from the
NAMD and VMD tutorials, available at
http://www.ks.uiuc.edu/Training/Tutorials/. This will give you an
initial parameter set and the knowledge you need to use it. Other charmm
parameters can be obained from the charmm website and/or google.
For building parameters, you'll want to look at the paratool plugin that
comes with VMD (http://www.ks.uiuc.edu/Research/vmd/plugins/paratool),
which will set up gaussian runs and do the analysis necessary for
parameterization. The methods for obtaining partial charges (and other
parameters) will be those used for the CHARMM forcefield, so you'll want
to look at the official CHARMM forcefield website
(http://www.pharmacy.umaryland.edu/faculty/amackere/force_fields.htm)
and references cited therein.
Best,
Peter
Francesco Pietra wrote:
> 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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