[gmx-users] PRODRG charges

[gpat at bioacademy.gr]

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?

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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