Hi francesco,
In case it helps -- you can still access "old" force fields that may seem
to have been deleted from Amber. Old force fields have not, in fact, been
deleted, but rather just moved to "oldff", mostly to prevent people from
running with outdated, deficient force fields (when much better
alternatives exist).
Using ff99SB directly is as easy as changing:
source leaprc.ff99SB
to
source oldff/leaprc.ff99SB
Hope this helps, and good luck,
Jason
On Mon, Jan 12, 2015 at 12:09 PM, Francesco Pietra <chiendarret.gmail.com>
wrote:
> Hi:
> That helped (and solved). I was using a leap ff from work I carried out
> years ago and, changing to ambertools14, I missed to update all the script.
> As I am normally faced with multichain systems, and have little patience to
> follow the residue renumbering to know where I am, I normally use other
> software. But this is no excuse for wasting your time, more importantly for
> renouncing to the great power of amber.
>
> Thanks
> francesco
>
> On Mon, Jan 12, 2015 at 5:31 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
> >
> > > On Jan 12, 2015, at 10:52 AM, Francesco Pietra <chiendarret.gmail.com>
> > wrote:
> > >
> > > I tried to follow correctly your kind suggestion
> > >
> > > In leap:
> > > parm10 = loadamberparams parm10.dat
> > > frcmod99SB = loadamberparams frcmod.ff99SB
> > > frcmodionsff99_tip3p = loadamberparams frcmod.ionsff99_tip3p
> > > frcmodzn = loadamberparams frcmod.MOL.known
> > > frcmodzn = loadamberparams frcmod.MOL.correspondence
> > > frcmodzn = loadamberparams frcmod.added_impr
> > > loadOff all_amino94.lib
> > > loadOff all_aminoct94.lib
> > > loadOff all_aminont94.lib
> > > loadOff ions94.lib
> > > loadOff solvents.lib
> >
> > Is there a reason you are trying to reinvent what the leaprc files do? I
> > would not suggest the current strategy that you are employing, since it
> is
> > way too easy to make a mistake. For instance -- parm10.dat contains the
> > frcmod.ff99SB modifications already, but I think some of the side-chain
> > atom types for the amino acids may be slightly different (in preparation
> > for the modifications that became ff12SB and ff14SB).
> >
> > Furthermore, the atom types used in parm10.dat correspond to the atom
> > typing used in amino10.lib, aminoct10.lib, and aminont10.lib, but you are
> > using the library files that were used for ff94 through ff99SB (excluding
> > ff03). Lastly -- and what is causing your error here -- you are using
> the
> > “old” definition of the ion residues/atom types (ions94.lib), whereas
> > frcmod.ionsff99_tip3p is designed to be used with atomic_ions.lib, if I’m
> > not mistaken.
> >
> > A lot of work has gone into refining the ion parameters, so all of the
> > atom types for these ions have been completely redone in a more sensible
> > way... but what this means is that the old library files and “new” frcmod
> > files are completely incompatible. The frcmod.ionsff99_tip3p file seems
> to
> > have been provided in order to allow the “old” (i.e., ff99-and-older) ion
> > parameters to be used with the “new” library files.
> >
> > The takeaway message here is: use the leaprc files that have been
> prepared
> > for you. Mixing and matching like you are doing here rarely results in
> > desired behavior, and I would discourage anybody from ever doing this.
> >
> > Good luck,
> > Jason
> >
> > --
> > Jason M. Swails
> > BioMaPS,
> > Rutgers University
> > Postdoctoral Researcher
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Jan 12 2015 - 09:30:03 PST
