Re: [AMBER] Force field ff99SB*-ILDN request

From: <>
Date: Wed, 17 Sep 2014 09:28:30 +0530

Hi Jason,

You are familiar with editing a topology file to a given force field type.
Could you please provide a tutorial may be on a tripeptide or tetrapeptide
which would be a simplified system. It will be very much useful to many
users. Further, it will reduce the incorporation of errors in the topology

Your help will be highly appreciated.


> On Sep 16, 2014, at 4:11 PM, David A Case <>
> wrote:
>>> On Sun, Sep 14, 2014 at 7:46 PM, David A Case
>>> <>
>>> wrote:
>>>> It can be tricky to get everything correct. The 2009 Best/Hummer
>>>> modifications involve only corrections to the psi angle, but you have
>>>> to
>>>> make sure that they are not applied to glycine or proline. I'm not
>>>> sure
>>>> that this can be done inside tleap without making some new atom types
>>>> that
>>>> are specific to GLY and PRO. This might be a place where a ParmEd
>>>> script
>>>> could be of real use.
>> I figured if I mentioned ParmEd, that Jason would have had a solution by
>> now. :-) Of course, as others have mentioned, the problem is not so
>> much
>> doing this (you could even hand-edit your ff99SB-ildn prmtop file to
>> make it
>> ff99SB*-ildn), as in making sure it agreed with GROMACS, or whatever
>> other
>> program (desmond?) provides the "reference implementation" for
>> ff99SB*-ildn.
> Haha. Well it _can_ be done with ParmEd. It has all of the functionality
> required to adjust parameters — setBond, setAngle, addDihedral, and
> deleteDihedral. And for certain classes of modifications you could
> implement the force field with a small number of ParmEd commands. If
> you’re modifying backbone dihedrals this becomes significantly harder to
> automate (because the selection masks will not be constant).
> If all of the modifications are intra-residue (like side chain torsions),
> then ParmEd may be the easiest solution. If not, then any ParmEd-based
> solution will have the same challenges as the “right” way to do it through
> tleap and frcmods.
>> Force field interoperability has made significant strides recently,
>> mostly by
>> programs that manipulate "low-level" descriptions like prmtop, PSF or
>> tinker
>> analyze files. There are lots of Google hits (including at the Amber
>> web
>> page) for programs to convert Amber topologies to Gromacs, but I'm not
>> personally aware of work in the other direction. (Pipe up if you know
>> how to
>> do this). That sort of tool would enable users to build the system in
>> Gromacs, then run it in Amber.
> This almost made it into ParmEd this summer, actually… my summer just
> ended 2 weeks too early :). To validate against GROMACS, you can always
> implement ff99SB*-ildn in Amber, convert the prmtop to GROMACS, and make
> sure they give exactly the same energies as the “reference” implementation
> for a wide array of systems.
> All the best,
> Jason
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
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Received on Tue Sep 16 2014 - 21:00:02 PDT
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