From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Fri May 11 2007 - 16:14:06 CDT
Thanks. I have examined the pages below from the point
of view that generating force field parameters for new
molecular entities is my unavoidable need (in fact,
DFT MD would be my way, it were not for the too short
trajectories and the inability to treat aromatics).
Because I use different codes than those suggested
below (Gaussian or Gamess), it seems that I can't make
use of paratool, unless there is a way to insert
manually what I can provide with my codes.
In the remote hypothesis that this is possible, I can
---Optimize the geometry by first global space search
mechanical tools and then QM at any level, also
calculating the trend of energy for dihedral values.
QM alone fails for the arrangement of atoms I am
---Calculate ESP, RESP, CRESP, or other types of
Partial Charges quite reliably at any basis set level
and getting that dipole moments for the assembly of
residues match those for the whole molecule.
--Any other type of QM calculation.
Is that possible?
--- Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
> 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
> 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
> and references cited therein.
> Francesco Pietra wrote:
> > New to the list and considering to download namd,
> > first I need information that I found difficult to
> > from the web site or archive list:
> > 1) Do Parameters come with namd download or
> > they be obtained elsewhere? In particular, how to
> > the latest CHARMM (or other) parameters as a
> > point?
> > 2) Where to obtain the list of CHARMM (or other)
> > to be used?
> > 3) Is any tool provided to build Parameters for
> > 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
> > provided by my quantum mechanical code?
> > It should be apparent from my questions that I
> > 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
> > why I mentioned CHARMM and nor AMBER.
> > Huge thanks for directing me to where such
> > can be found.
> > francesco pietra
> > __________________________________________________
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