Dear James,
> 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
"LJ interactions were computed using a cutoff of 1.0 nm, and the
electrostatic interactions were treated using PME with the same
real-space cutoff."
In this paper the authors use Gromacs; I thought you use AMBER...
> 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?
I am sure people in this list are more qualified than me to discuss
about this parameter; or may be - as it is related to Gromacs post
your query in the Gromacs mailing list...
regards, Francois
> 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 - 23:30:02 PDT
