Many thanks! I suspected there was a silent formatting issue somewhere,
since the problem was with the 10000th water. The jobs work perfectly now
(for the other step2_*psf files with EXT).
Best,
Pete
On Sat, Nov 1, 2014 at 6:35 PM, Jason Swails <jason.swails.gmail.com> wrote:
>
> > On Oct 31, 2014, at 4:36 PM, Pete Kekenes-Huskey <huskeypm.gmail.com>
> wrote:
> >
> > Hi Jason,
> > Thanks for your continued help. We have made progress with your
> > suggestions, but are still confronting problems with SHAKE. Namely,
> > minimization/equilibration appear to run fine with pmemd (mpi), but the
> > same equilibration procedure fails with pmemd.cuda (Amber 14):
> >
> > 785: 31632 - 31633 and 787: 31633 - 31634
> >
> > Hydrogen atom 31633 appears to have multiple bonds to atoms 31632 and
> 31634
> > which is illegal for SHAKEH.
> >
> > Exiting due to the presence of inconsistent SHAKEH hydrogen clusters.
> >
> > I've verified that the guilty hydrogen should indeed be bonded to both
> the
> > oxygen and opposing hydrogen (vmd output below) and that the geometry
> > appears normal. Oddly, this error is thrown for the TIP3 water with resid
> > 10001, so there are 10K TIP3 waters before that entry that appear to be
> ok.
> > The .in file we ran was the following:
> >
> > &cntrl
> >
> > imin = 0,
> >
> > irest = 0,
> >
> > ntx = 1,
> >
> > ntb = 1,
> >
> > cut = 10,
> >
> > ntr = 1,
> >
> > ntc = 2,
> >
> > ntf = 2,
> >
> > ig=-1,
> >
> > tempi = 0.0,
> >
> > temp0 = 300.0,
> >
> > ntt = 3,
> >
> > gamma_ln = 1.0,
> >
> > nstlim = 1000, dt = 0.002,
> >
> > watnam='TIP3',OWTNM='OH2',
> >
> > hwtnm1='H1',hwtnm2='H2',
> >
> > ntpr = 100, ntwx = 100, ntwr = 1000
> >
> > /
> >
> > Hold the protein fixed with weak restraints
> >
> > 10.0
> >
> > RES 1 90
> >
> > END
> >
> > END
> >
> > /////
> >
> > I've uploaded all the files we've used to
> > http://users.mccammon.ucsd.edu/~huskeypm/share/filez.tgz. To
> summarize, we
> > created the input files with CHARMM-GUI (in order to be consistent with
> > previous runs) and the charmm-36 FF. We used parmed (latest version from
> > the git repo) to obtain prmtop/inpcrd files:
> >
> > chamber -top toppar/top_all36_prot.rtf -param toppar/par_all36_prot.prm
> > -str toppar/toppar_water_ions.str -psf step2_solvator.xplor.psf -crd
> > step2_solvator.crd -box 80.,80.,80.
> >
> > outparm apo.prmtop apo.inpcrd
> >
> > Minimizations were done using pmemd. All input files should be in the
> link
> > I provided above.
> >
> > If you're able to look into this and get this running via pmemd.cuda,
> we'd
> > be very grateful. I'm sure were missing something subtle, so a third pair
> > of eyes would be helpful.
>
> OK, so this was a very weird problem. The problem is with
> step2_solvator.xplor.psf. This PSF file is not “extended” (note the lack
> of EXT in the top line, which is present in the other step2_*.psf files),
> which means the residue number field can have at most 4 characters (so no
> chain can have more than 9999 residues). Look around line 31637 of
> step2_solvator.xplor.psf, where it appears that the last digit on the
> residue number is simply shaved off (so that 10 water residues are
> conflated into the single residue 10000).
>
> As a result, ParmEd puts these 30 atoms into a single residue (since
> that’s what the PSF files tells it to do). To pmemd.cuda, this does not
> look like a water (that should be single residues of exactly 3 atoms). As
> a result, those constraints do not get dispatched to the fast SETTLE
> routines and the “slow” (i.e., approximate, iterative SHAKE) routine in
> pmemd.cuda is _not_ generalized to handle hydrogen bonded to more than one
> atom.
>
> The solution is to use literally _either_ of the other two step2_solvator
> PSF files (which are extended). :) I tested it with both options and it
> solved the problem you were seeing on my machine with pmemd.cuda.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
======================
Peter Kekenes-Huskey, Ph.D.
Assistant Professor
Department of Chemistry
University of Kentucky
http://pkh.as.uky.edu/
======================
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Received on Sun Nov 02 2014 - 17:30:02 PST
