Is there a reason you cannot (or do not want to) convert the same starting
coordinates/topologies between the two programs?
I know that many people/groups have developed fairly robust conversion
scripts for AMBER/GROMACS (off the top of my head I believe I recall
Michael Shirts distributing a Perl script for this, but that was probably a
decade ago).
Regards,
Brian
P.S. Another alternative that I have used for non-orthorhombic/octahedral
boxes is to build a water box first (for some reason I always used VMD for
this) and just concatenate the solute/solvent before loading into tleap.
Your molecule will of course not be "solvated" as such due to overlaps, but
you can delete waters etc. This is not a quick solution, but it works with
enough patience.
On Wed, Jun 18, 2014 at 9:43 AM, newamber list <newamberlist.gmail.com>
wrote:
> Hi All
>
> Thanks for you replies. Yes I agree choosing same number of water and box
> shape initially should converge to similar final equilibrated densities and
> volumes with Amber and Gromacs. But I would like to know how AMBER differs
> in adding waters compared to Gromacs as a initial guess (earlier I copied
> mail from Gromacs archive explaining how initial water box is created by
> Gromacs)
>
> Thanks
>
>
> On Sun, Jun 15, 2014 at 4:52 PM, David A Case <case.biomaps.rutgers.edu>
> wrote:
>
> > On Sun, Jun 15, 2014, newamber list wrote:
> >
> > > command: solvateoct hex20 TIP3PBOX 12.0
> >
> > Note that this command is only intended to give a *very rough* starting
> > structure for further simulation. The number of water molecules chosen
> > for a
> > given box size (or buffer size) will be very different from what you will
> > get
> > after equilibration: the number of waters will stay the same (of course),
> > but
> > the size of the box will change a lot.
> >
> > If you choose the same number of waters in Gromacs and Amber, and
> simulate
> > to
> > equilibrium at some temperature, you should get the same average
> properties
> > (such as density). In Amber, at least, the equilibrated density will be
> > very
> > different than the initial density. No one in the Amber community has
> not
> > (yet) felt a big need to improve the initial guess that LEaP provides.
> >
> > ....dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for
Integrative Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
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Received on Wed Jun 18 2014 - 07:30:03 PDT
