[gmx-users] PRODRG charges

[Mark Abraham]

On 12/01/2012 10:42 PM, gpat at bioacademy.gr wrote:
> Hi
>
> Many thanks for your reply and sorry to come back on this.
>
> Is the fitting to experimental free energies of solvation, the
> only acceptable way to get "GROMOS-compatible charges"? Acceptable
> because this is the way that partial charges were derived for the
> gromos ff.
>
> In the quite usual case that these experimental data are not available
> for the ligand one is interested in, are DFT/ESP charges acceptable?

Possibly, but you'd have a higher burden of proof that your simulation 
is a valid model of reality then if the parametrization was consistent. 
This trade-off could well drive the choice of a different force field.

Mark

>
> Thanks again.
> George
>
>>
>> gpat at bioacademy.gr wrote:
>>> Hello
>>>
>>> Given that the partial charges from PRODRG are not reliable (as
>>> explained
>>> Justin Lemkul's paper),
>>> are AM1-BCC charges calculated with the Chimera/Amber Tools a reasonable
>>> starting point?
>>>
>> Yes, those charges are a reasonable start, but will almost certainly not
>> be
>> sufficient for the final topology.
>>
>>> In this case, do we treat all ligand atoms as one charge group?
>>>
>> Unless your ligand is 4 atoms or less, no.  Please consult the manual
>> regarding
>> charge groups, and see existing Gromos96 building blocks for suitable
>> charge
>> groupings.
>>
>> -Justin
>>
>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> 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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>