Hello Dr. Case and Dr. Ponder,
Unfortunately simply removing the lines still screws up tinker_to_amber
parsing since now there are less multipole entries than is specified in the
header of the analout file. If I change the header from " Polarizable
Multipoles 136" to " Polarizable Multipoles 133" then the conversion
completes. But that means that I don't get multipole data for the disulfide
bridge atoms.
My other approach was to copy the multipole values from extended-chain
structure into the analout for the folded + bridged structure, but because
of two extra H in CYS vs CYX, the atom numbers don't line up. If I use CYX
instead of CYS in the extended structure the valence gets all wonky but I
get multipole data for atoms 9 and 90. Atom 2, even without explicit
bridge, still has the weird zero multipole entry. In other words, I have
not been able to get a working, even if hacky, solution to the problem.
I'll try to run the prmtop+inpcrd with removed zero-multipole through
Sander's analysis to get an energy and compare it to Tinker's.
Thank you,
Eugene Yedvabny
On Sat, Dec 14, 2013 at 8:09 AM, case <case.biomaps.rutgers.edu> wrote:
> On Fri, Dec 13, 2013, Eugene Yedvabny wrote:
> >
> > I am still stuck with Amber -> Tinker -> Amber conversion necessary to
> get
> > Amoeba prmtop and inpcrd. It appears that my first assumption about NHE
> ->
> > NH2 conversion being the culprit is wrong. The error is actually caused
> by
> > the disulfide bridge: Tinker recognizes CYX residues and automatically
> > makes a bond between them (yay!) but then analyze.x chokes on the
> > multipoles for that bridge (nay!):
> >
> > Atomic Multipole Parameters :
> >
> > Atom Coordinate Frame Definition Multipole Moments
> > 2 2 0 0 0.00000
> > 0.00000 0.00000
> 0.00000
> > 0.00000
> > 0.00000 0.00000
> > 0.00000 0.00000
> 0.00000
> >
> > I am attaching the whole analout file, but the above is an example of a
> > section that confused tinker_to_amber.
>
> Thanks for finding this! It looks like somehow it should be easy to fix.
>
> I'm cc-ing this to Jay Ponder to see if this is what is expected for S-S
> bonds.
>
> Try this: remove the lines like those above, and re-run tinker_to_amber.
> Do
> you get the same energies then in tinker and in pmemd.amoeba or sander?
>
> It's easy enough to change tinker_to_amber to handle this, if that is what
> needs to be done.
>
> ...regards...dac
>
>
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Received on Sat Dec 14 2013 - 16:30:02 PST
