Hi,
> "my intention is NOT to run REMD. I do not want to titrate any of the
> ionisable residues.
>
> I want to run a traditional MD simulation at pH=4.0"
>
Why not determine what the protonation states of your residues would be at
pH=4.0 and run standard MD (not constant pH MD), at least as an initial
test.
Presumably, many of the histidines would be doubly protonated, and perhaps
some glutamate / aspartates as well.
--Marc
>
> On May 11, 2012, at 2:40 PM, Jason Swails wrote:
>
> >
> >
> > On May 11, 2012, at 8:32 AM, George Tzotzos <gtzotzos.me.com> wrote:
> >
> >> Hi Jason,
> >>
> >> I'm attaching the input file as per your request. I think you will
> recognise it (http://jswails.wikidot.com/ph-replica-exchange).
> >
> > Ah, pH remd is not part of Amber 12. I added it to sander shortly after
> 12 was released (it's actually not even in the main developer branch yet,
> although it will be soon).
> >
> > I will probably post a pure constant pH MD tutorial sometime this summer
> somewhere on either ambermd.org or my wiki.
> >
> > Thanks!
> > Jason
> >
> >>
> >> Best regards
> >>
> >> George
> >>
> >>
> >>
> >> On May 11, 2012, at 2:29 PM, Jason Swails wrote:
> >>
> >>> The problem is in your input file, so it would help if you attached
> that instead.
> >>>
> >>> --
> >>> Jason M. Swails
> >>> Quantum Theory Project,
> >>> University of Florida
> >>> Ph.D. Candidate
> >>> 352-392-4032
> >>>
> >>> On May 11, 2012, at 5:30 AM, George Tzotzos <gtzotzos.me.com> wrote:
> >>>
> >>>> I'm trying to minimise the structure of a protein-ligand complex for
> constant pH simulations.
> >>>>
> >>>> Running: mpirun -np 12 sander.MPI -O -i min.in -o min.out -p
> complex.prmtop -c complex.inpcrd -r min.rst -ref complex.inpcrd
> >>>>
> >>>> gives the following error message:
> >>>>
> >>>> "At line 1019 of file _mdread.f (unit = 5, file = 'min.in')
> >>>> Fortran runtime error: End of file
> >>>> APPLICATION TERMINATED WITH THE EXIT STRING: Hangup (signal 1)"
> >>>>
> >>>> I'm attaching the md.out file hoping that someone could help me to
> sort out this problem.
> >>>>
> >>>> Best regards
> >>>>
> >>>> George
> >>>>
> >>>> <min.out>
> >>>> _______________________________________________
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> >>>
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> >>
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Received on Fri May 11 2012 - 06:30:04 PDT
