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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > 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 - 07:00:02 PST
