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
> >
> >
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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>
--
======================================================================
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 - 00:30:03 PDT
