Hi Eugene,
I realize this is a very old thread (regarding the use of
tinker_to_amber to convert a small peptide to an amber topology) in
which you were having some trouble with the analout file being produced
by Tinker.
I revisited your system using the current Tinker release (6.3) and going
back to your original oxy.key and oxy.pdb files you posted here:
(
http://archive.ambermd.org/201312/0121.html). After changing the
parameter keyword in the .key file to point to my version of the
parameter file, I am able to build the amoeba prmtop with
tinker_to_amber without any problems. Here was my sequence, starting
with your oxy.pdb file exactly:
pdbxyz oxy
analyze oxy PC > oxy.analout
tinker_to_amber -name oxy -title "test oxy"
I've attached a zip archive of oxy.prmtop and oxy.inpcrd in case they
are helpful. Perhaps all you need to do is update to the latest
Tinker...
HTH,
Jason
On Sat, 2013-12-14 at 16:01 -0800, Eugene Yedvabny wrote:
> 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
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
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--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Feb 07 2014 - 12:00:03 PST
