This file was generated as the output of a constant-pH run, using the
scripts provided in the constant-pH tutorial on Amber.
That's very interesting: I just looked at the file more closely, and it
appears that the STATEINF states after 20 are empty and just list (0) for
all the numbers. I will see what happens if I delete those.
On Mon, Aug 24, 2020, 8:57 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> Thanks for the files.
>
> How exactly did you generate the CPIN file (dio1.mono.cpH.md4.cpin)?
> Indeed, it does appear to describe 50 residues (the index for STATEINF
> goes from 0 to 49) but TRESCNT is 21, not 50. Unless I'm missing
> something about the CPIN format, I think this CPIN file is invalid.
>
> -Dan
>
> On Tue, Aug 18, 2020 at 9:02 AM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> >
> > Hi,
> >
> > Could you send me (off-list) the CPIN file in question? Also, I'm sure
> > that the CPOUT files are probably too large, but could you try to send
> > even a portion of them? In addition, maybe send the topology and
> > restart file as well. Any additional information (AmberTools/cpptraj
> > version etc) will be helpful. Thanks,
> >
> > -Dan
> >
> > On Sat, Aug 15, 2020 at 10:32 AM Jonee Lillard <jonelil.mail.regent.edu>
> wrote:
> > >
> > > Dear Sir or Madam:
> > >
> > > I have been running three rather long constant-pH simulations of a
> > > 164-residue protein. The simulations have been going fine, but their
> output
> > > has been mostly unanalyzable. Attached is the input file I have been
> using
> > > for the simulations.
> > >
> > > The first four production runs of each simulation have worked fine in
> the
> > > command-line cphstats functionality specified in Tutorial 18. However,
> the
> > > fifth and subsequent runs produce the following error:
> > >
> > > $cphstats -i dio1.mono.cpH.md4.cpin dio1.mono.cpH.md5.cpout -o
> > > md5.calcpka.dat
> > >
> > >
> > > *Did not recognize the format of cpout dio1.mono.cpH.md5.cpout.Error:
> Cpout
> > > file dio1.mono.cpH.md5.cpout is invalid! Skipping.Error: Number of
> Cpout
> > > files 0 does not equal number specified: 1*
> > >
> > > Attempting to run them in CPPTRAJ does not work and yields the
> following
> > > error, though this seems to be dependent on the format of the .cpin
> files
> > > rather than the .cpout files.
> > >
> > > >readdata dio1.mono.cpH.md5.cpout cpin dio1.mono.cpH.md4.cpin
> > > [readdata dio1.mono.cpH.md5.cpout cpin dio1.mono.cpH.md4.cpin]
> > > Reading 'dio1.mono.cpH.md5.cpout' as Amber CPOUT with name
> > > 'dio1.mono.cpH.md5.cpout'
> > > System: Unknown
> > > Error: Number of states in CPIN (50) != TRESCNT in CPIN (21)
> > > Error: Could not read CPIN file 'dio1.mono.cpH.md4.cpin'
> > > Error: reading datafile dio1.mono.cpH.md5.cpout
> > > Error: Could not read data file 'dio1.mono.cpH.md5.cpout'.
> > >
> > > Attempting to use cphstats in CPPTRAJ results in this error.
> > > > cphstats -dio1.mono.cpH.md4.cpin dio1.mono.cpH.md5.cpout name
> > > md5.calcpka.dat
> > > [cphstats -dio1.mono.cpH.md4.cpin dio1.mono.cpH.md5.cpout name
> > > md5.calcpka.dat]
> > > Warning: '-dio1.mono.cpH.md4.cpin' selects no data sets.
> > > Warning: 'dio1.mono.cpH.md5.cpout' selects no data sets.
> > > Error: No pH data sets.
> > > Error: Could not setup analysis [cphstats]
> > >
> > > I have also noticed that the numbering of the time values in the fifth
> and
> > > subsequent .cpout files runs out of characters in the file template
> and has
> > > asterisks instead. Could this be responsible for the failure of
> > > recognition, and if so, how can it be fixed or circumvented, whether
> > > through the command line or CPPTRAJ?
> > >
> > > -- Jonee
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Aug 25 2020 - 08:30:03 PDT
