I used Amber18.17. All the files were made using the leaprc.constpH force
field.
On Tue, Aug 25, 2020, 3:26 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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
> > >> > > _______________________________________________
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Received on Wed Aug 26 2020 - 06:30:03 PDT
