Dear Francois,
thank you for so detailed response! In literature I've found the usage of
1.0 nm cutofs with the berger lipids
http://pubs.acs.org/doi/abs/10.1021/ct200491c
by the way during my simulation with such cutofs I've observed decreased of
my system in the Z-direction ( I've observed the same also during
simulation of such systems in the Charm full atomic ff with the same
cut-offs but not in gromos united-atom ff where I used 1.2 cutoffs). Might
the increasing of cutoffs up to 1.2 nm solve this problem?
James
2013/4/9 FyD <fyd.q4md-forcefieldtools.org>
> Dear James,
>
> > I want to perform list of full atomic simulation of protein-ligand
> > complexes in Gromacs using Amber99sb force field and ligand parametrized
> by
> > means of antechamber (acpype).
> >
> > 1- From antechamber tutorials I've found that GAFF is used for such
> ligand
> > parametrization. What cut-offs for electrostatics as well as vdw should I
> > use for the modelling of protein-ligand complexes ? (assuming that I've
> > used 1.0 cutoffs with such systems without ligands)
>
> 'cutoffs of 1.0' seems quite small - what about using the default value?
> I am sure you can find discussions in the Amber mailing list archive
> about cutoff values...
>
> > 2- How I can assign charges more carefully ?
>
> More carefully than 'what'? Antechamber handles various models of
> atomic charges; RESP, ESP?, AM1-BCC, Mulliken?
>
> You might be interested in using the R.E.D. tools and/or R.E.D. Server
> to derive RESP or ESP (i.e. molecular electrostatic based) charge
> values...
>
> > Could you provide me with
> > some example of such charges assignment based on different chemical
> > compounds?
>
> The 'building block' approach developed in the R.E.D. tools and/or
> R.E.D. Server has been specially designed for deriving charge values
> for a set of molecules belonging to a family of molecules with common
> and variable parts.
>
> Let's take an example of 10 molecules with the R1 common part and the
> S1-S10 variable parts:
> R1-S1
> R1-S2
> ...
> R1-S10
>
> Using R.E.D. one can derive charge values for these 10 molecules by
> defining 11 elementary building blocks:
>
> R1-x y-S1 (x & y are the connecting groups)
> R1-x y-S2
> ...
> R1-x y-S10
>
> By defining specific charge constraints for the x and y connecting
> groups one can generate the R1 and S1-S10 molecular fragments that are
> combined into the 10 wanted/target molecules:
>
> R1 + S1 ---> R1-S1
> R1 + S2 ---> R1-S2
> ...
> R1 + S10 ---> R1-S10
>
> In this approach the conformation(s) of the R1-x and y-S1/10 building
> blocks is/are fully controlled, the geometry optimization step is
> often far shorter and the charges for the R1 group are empirically
> defined and are common in the R1-S1/R1-S10 molecules...
>
> regards, Francois
>
>
>
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Received on Tue Apr 09 2013 - 23:00:02 PDT
