[gmx-users] PRODRG charges

[David van der Spoel]

On 2012-01-12 12:42, 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?
>
No. CHeck http://compbio.biosci.uq.edu.au/atb/


> 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
>>
>> ========================================
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>


-- 
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