What version of Amber did you use? The cpin file has more issues than
I noticed at first. It's missing the STATEENE variable (which is what
is confusing the cpptraj CPIN parser), and CPH_IGB/CPHFIRST_SOL are
set to 0.
-Dan
On Tue, Aug 25, 2020 at 11:31 AM Jonee Lillard <jonelil.mail.regent.edu> wrote:
>
> Deleting the empty STATEINF slots, as attached below, and running it in
> CPPTRAJ produced a different error:
>
> > readdata dio1.mono.cpH.md5.cpout cpin md4.test.cpin
> [readdata dio1.mono.cpH.md5.cpout cpin md4.test.cpin]
> Reading 'dio1.mono.cpH.md5.cpout' as Amber CPOUT with name
> 'dio1.mono.cpH.md5.cpout'
> System: Unknown
> Error: Number of residues in CPIN (22) != TRESCNT in CPIN (21)
> Error: Could not read CPIN file 'md4.test.cpin'
> Error: reading datafile dio1.mono.cpH.md5.cpout
> Error: Could not read data file 'dio1.mono.cpH.md5.cpout'.
>
> On Tue, Aug 25, 2020 at 11:22 AM Jonee Lillard <jonelil.mail.regent.edu>
> wrote:
>
> > 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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> >>
> >
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Received on Tue Aug 25 2020 - 12:30:02 PDT
