you're right, it looks like those are in nm. The link I gave will tell you
the units that are used in Amber inputs, and those correspond to the
published values for ff14SB and the numbers in the force field files that
are provided in the free download of AmberTools (
http://ambermd.org/AmberTools.php).
When it's ported to other programs, the units may change, so it's best to
see what units are expected in the inputs for those programs. If your
original question is about the units expected by openMM (which is what the
Chodera lab's port of ff14SB looks like it belongs to), you might want to
check this link for openMM units:
http://docs.openmm.org/6.1.0/userguide/application.html
The Amber home page also gives links to other pages that describe how to
use the Amber force fields in many other programs, including openMM:
http://ambermd.org/AmberModels.php
hope that's helpful.
On Mon, Feb 5, 2018 at 11:15 AM, Siddhartha Jain <tmfs10.gmail.com> wrote:
> I'm not sure whether that's the same units. For example, for the harmonic
> bond force, the website says [1] the equilibrium length is in angstroms.
> However the C-C bond length for example is listed as 0.1525. The C-C bond
> length (in diamond) is 154 pm or 0.154 nm leading me to suspect that the
> bond length given is in nm, contrary to the what it says on the website you
> linked.
>
> Thanks,
> --Sid
>
>
> [1]
>
> - 4 - ***** INPUT FOR BOND LENGTH PARAMETERS *****
>
> IBT , JBT , RK , REQ
>
> FORMAT(A2,1X,A2,2F10.2)
>
> IBT,JBT Atom symbols for the two bonded atoms.
>
> RK The harmonic force constant for the bond "IBT"-"JBT".
> The unit is kcal/mol/(A**2).
>
> REQ The equilibrium bond length for the above bond in
> Angstroms
>
> The input is terminated by a blank card.
>
>
>
>
> On Mon, Feb 5, 2018 at 11:06 AM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > it looks like they are just reporting the standard parameters from
> ff14SB.
> > You can look on the Amber web site for descriptions of our force field
> > fields and the units.
> > http://ambermd.org/formats.html#parm.dat
> >
> >
> > On Sun, Feb 4, 2018 at 5:16 PM, Siddhartha Jain <tmfs10.gmail.com>
> wrote:
> >
> > > Hi,
> > >
> > > What are the units used in the ff14sb force field xml file (
> > > https://github.com/choderalab/openmm-forcefields/blob/
> > > master/amber/ffxml/ff14SB.xml
> > > )?
> > >
> > > Thanks!
> > > _______________________________________________
> > > 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
> >
>
>
>
> --
> https://tmfs10.github.io
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Feb 05 2018 - 09:00:02 PST
