[gmx-users] PRODRG charges
David van der Spoel
spoel at xray.bmc.uu.se
Thu Jan 12 13:04:19 CET 2012
On 2012-01-12 12:42, gpat at bioacademy.gr wrote:
> 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?
No. CHeck http://compbio.biosci.uq.edu.au/atb/
> Thanks again.
>> gpat at bioacademy.gr wrote:
>>> Given that the partial charges from PRODRG are not reliable (as
>>> 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
>> 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
>> charge groups, and see existing Gromos96 building blocks for suitable
>> 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
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David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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