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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> > > >
> > > >
> > > > --
> > > > *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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> > http://lists.ambermd.org/mailman/listinfo/amber
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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
