Lucio Ricardo Montero Valenzuela wrote:
The target forcefield will be G43a1. But I would move to more recent
versions of GROMOS 53a5 or 53a6.
A more empirical charge assignment is often a reasonable starting point for
assigning GROMOS charges. As I understand it, quantum calculations were only
done to get electron densities around each atom in various functional groups;
the subsequent parameterization was done empirically. You must then verify that
the parameters match some condensed-phase criteria (the force field references
will tell you what types).
I have gotten reasonable results based on assigning charges from comparable
functional groups within the building blocks in, i.e. ffG53a6.rtp.
-Justin
El jue, 04-06-2009 a las 16:29 +1000, Mark Abraham escribió:
Lucio Ricardo Montero Valenzuela wrote:
I want to run a MD in an unparameterized molecule similar to adenine. I can get
the approximated parameters in PRODRG. But I have read that PRODRG not always
give the correct charge. Is it a good idea to replace that charges using the
charges given with the R.E.D.vIII using ESP-A1 (suitable for AMBER, GLYCAM and
OPLS forcefields)?. Or will it be mixing forcefields?.
That depends on your target forcefield for your MD.
Mark
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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