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 Mon Aug 24 2020 - 18:00:02 PDT
