I still think it's worth trying to simulate what is in the crystal. Or
maybe take your restart from longer md in ff14SB and switch to ff19SB. GPUs
can be finicky with high energies from poor initial models. Not sure why
capped vs not matters - that shouldn't change any usage of ff19SB. Is he
problem reproducible in capped vs uncapped? Just trying to think of
explanations...
On Wed, Dec 11, 2019, 11:51 AM Pavlína Pokorná <pokorna.pavlina.ibp.cz>
wrote:
> I don’t think this is the problem as the same structure without end-caps
> runs OK. I also had the same issue with second system I tested (another
> protein, a bit lower resolution), which didn’t contain any other
> modifications wrt crystal structure than the end-caps...
>
> On Wed, 11 Dec 2019 at 16:08, Carlos Simmerling <
> carlos.simmerling.gmail.com>
> wrote:
>
> > maybe you can try first without the mutations, so you know that the
> initial
> > model is good?
> >
> > On Wed, Dec 11, 2019 at 9:40 AM Pavlína Pokorná <pokorna.pavlina.ibp.cz>
> > wrote:
> >
> > > yes, it is based on X-ray structure with 1.8A resolution but few
> > > solvent-exposed residues are mutated.
> > >
> > >
> > > On Wed, Dec 11, 2019 at 3:04 PM Carlos Simmerling <
> > > carlos.simmerling.gmail.com> wrote:
> > >
> > > > What is the initial model? Is it an experimental structure?
> > > >
> > > > On Wed, Dec 11, 2019, 8:35 AM Pavlína Pokorná <
> pokorna.pavlina.ibp.cz>
> > > > wrote:
> > > >
> > > > > Dear Carlos,
> > > > >
> > > > > thanks for your reply, I was not aware of this. I use equilibration
> > > > > protocols with gradual heating and decrement of heavy-atom
> restraints
> > > > > followed by a 1 ns of unbiased simulation run before starting cuda
> > > > > simulations. So I guess the structure should be well-equilibrated.
> > > > Still, I
> > > > > can try to modify my setup to give the system more time to
> > equilibrate.
> > > > >
> > > > > Regards,
> > > > > Pavlina
> > > > >
> > > > > On Wed, Dec 11, 2019 at 12:57 PM Carlos Simmerling <
> > > > > carlos.simmerling.gmail.com> wrote:
> > > > >
> > > > > > We haven't seen problems with standard caps - they actually use
> > > ff14SB
> > > > so
> > > > > > should not be a problem. There are times when a poor quality
> > > structure
> > > > > may
> > > > > > just be ok with Cuda for ff19SB but not ff14SB (or vice versa) -
> is
> > > > this
> > > > > > for a well equilibrated system?
> > > > > >
> > > > > > On Wed, Dec 11, 2019, 5:38 AM Pavlína Pokorná <
> > > pokorna.pavlina.ibp.cz>
> > > > > > wrote:
> > > > > >
> > > > > > > Dear all,
> > > > > > >
> > > > > > > when attempting simulations with ff19SB with the updated
> Amber18
> > > > > version
> > > > > > > from Carlos Simmerling's GitHub, I failed to run pmemd.cuda
> > > > simulations
> > > > > > > with ACE and NHE caps on N- and C- termini of the protein.
> > > > Simulations
> > > > > > > crashed with the following error in ~50 nanoseconds: "Error: an
> > > > illegal
> > > > > > > memory access was encountered launching kernel kNLSkinTest". No
> > > > further
> > > > > > > error message is printed in the simulation *.out file and the
> > > > > last-saved
> > > > > > > structure showed no abnormalities. Simulations with the same
> > system
> > > > > > without
> > > > > > > the end-caps run without any problems. Runs with the end-caps
> > with
> > > > > sander
> > > > > > > on CPUs do not result in this error. Test ff14SB cuda
> simulations
> > > > with
> > > > > > the
> > > > > > > end-caps with the updated Amber18 run also without problems. I
> > have
> > > > > ~1100
> > > > > > > atoms in my system.
> > > > > > >
> > > > > > > It seems that cuda + ff19SB + caps combination produces some
> > large
> > > > > > numbers
> > > > > > > somewhere. Is there something I am missing or could you advise
> > any
> > > > > > possible
> > > > > > > solution to my problem?
> > > > > > >
> > > > > > > The ff19SB improved some local backbone conformations (and
> > > associated
> > > > > > > protein-protein interactions) wrt ff14SB in my protein-protein
> > > > complex,
> > > > > > so
> > > > > > > I'd like to use this force field. Still, I need to use the
> > end-caps
> > > > due
> > > > > > to
> > > > > > > the excessive and undesired end-end interactions in the
> > structure.
> > > > > > >
> > > > > > > I'd be grateful for any comment.
> > > > > > >
> > > > > > > Best wishes,
> > > > > > > Pavlina
> > > > > > >
> > > > > > > --
> > > > > > > Pavlina Pokorna
> > > > > > > *PhD student*
> > > > > > > Institute of Biophysics of the CAS, v. v. i.
> > > > > > > Kralovopolska 135, 612 65 Brno
> > > > > > > _______________________________________________
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> > > > > > >
> > > > > > _______________________________________________
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> > > > >
> > > > >
> > > > > --
> > > > > *Mgr. Pavlína Pokorná*
> > > > > *PhD student*
> > > > > Institute of Biophysics of the CAS, v. v. i.
> > > > > Kralovopolska 135, 612 65 Brno
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> > >
> > >
> > > --
> > > *PhD student*
> > > Institute of Biophysics of the CAS, v. v. i.
> > > Kralovopolska 135, 612 65 Brno
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> --
> *PhD student*
> Institute of Biophysics of the CAS, v. v. i.
> Kralovopolska 135, 612 65 Brno
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Received on Wed Dec 11 2019 - 09:00:02 PST
