So I'm trying to write a program to read in the FF file myself so I need to
know the units used in the actual file. In which file are the parameters
amber itself uses?
--Sid
On Mon, Feb 5, 2018 at 11:30 AM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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!
> > > > _______________________________________________
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> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > https://tmfs10.github.io
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> >
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Received on Mon Feb 05 2018 - 09:00:03 PST
