From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Tue May 08 2007 - 17:01:40 CDT
The quickest answer for most of what you ask is here:
Typically, we use top/par all27 prot_lipid or prot_na.rtf/inp (yes,
their naming convention is a little overwhelming at first). Also, he
has some (somewhat scattered) papers/presentations on the force field
and how it was parameterized.
VMD has a couple tools, molefacture and paratool, to build and
parameterize new molecules; there are pages for these linked from the
VMD page ( www.ks.uiuc.edu/Research/vmd/plugins ). The guide to
paratool in particular may be easiest to understand regarding the
basics of force field parameterization for charmm.
You will also likely find the tutorials listed on our web site
( www.ks.uiuc.edu/Training/Tutorials ) very helpful in getting started.
On May 8, 2007, at 4:46 PM, 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
> 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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