Dear all,
yes, I'm using Gromacs with Amber99sb force field and berger lipids adapted
for this ff.
In gromacs vdw and electrostatics cut-offs set to the 1.0 nm (10
angstroems).
What cut-offs have u used in the amber during simulation of the membrane
proteins?
James
2013/4/10 Astrid Maaß <astrid.maass.scai.fraunhofer.de>
> Dear James,
>
> To my knowledge the default unit for distances in Amber is Angstroem, in
> contrast to the one in Gromacs, which is nm. So, a cutoff of 1.0 nm equals
> 10.0 Angstroem, which may be more appropriate to prevent the unwanted
> behavior.
>
> HTH
> Astrid
>
>
>
> ----- Ursprüngliche Mail -----
> > Von: "James Starlight" <jmsstarlight.gmail.com>
> > An: "AMBER Mailing List" <amber.ambermd.org>
> > Gesendet: Mittwoch, 10. April 2013 07:33:39
> > Betreff: Re: [AMBER] on the usage of Antechamber for the ligand
> parametrisation
> >
> > 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
> > >
> > >
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
> --
> ======================================================================
> Dr. Astrid Maass
> Fraunhofer-Institute for Algorithms and Scientific Computing (SCAI)
> Schloss Birlinghoven
> D-53754 Sankt Augustin, Germany
>
> http://www.scai.fraunhofer.de
>
> Phone: +49 - 2241 - 14 - 2481
> Fax: +49 - 2241 - 14 - 2181
> E-mail: astrid.maass.scai.fraunhofer.de
> ======================================================================
>
>
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Received on Wed Apr 10 2013 - 00:30:04 PDT
