[gmx-users] Replacing the PRODRG charges

[Justin A. Lemkul]

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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-- 
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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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