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
file.
Your help will be highly appreciated.
Best,
Sunita
>
> On Sep 16, 2014, at 4:11 PM, David A Case <case.biomaps.rutgers.edu>
> wrote:
>
>>> On Sun, Sep 14, 2014 at 7:46 PM, David A Case
>>> <case.biomaps.rutgers.edu>
>>> 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
