it was reproducible in several simulations of the two systems I tested.
Many thanks for your ideas, I’ll try them and let you know the results.
On Wed, 11 Dec 2019 at 17:55, Carlos Simmerling <carlos.simmerling.gmail.com>
wrote:
> 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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> > > > > >
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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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
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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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Received on Wed Dec 11 2019 - 09:30:02 PST
