Sorry for the delay on this. Expecting an addition to the family this
week so my schedule has been a little crazy. I'm looking at it now.
-Dan
On Sat, Aug 22, 2020 at 9:05 AM Jonee Lillard <jonelil.mail.regent.edu> wrote:
>
> I sent you the files off-list on Tuesday. The versions of CPPTRAJ and
> AmberTools are 4.14.0 and 19.09 respectively.
>
> -- Jonee
>
> On Tue, Aug 18, 2020 at 9:37 AM Jonee Lillard <jonelil.mail.regent.edu>
> wrote:
>
> > The cpptraj version I have been using is v.4.14.0; the AmberTools version
> > is 19.09
> >
> > The requested files are attached below.
> >
> > On Tue, Aug 18, 2020 at 9:03 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
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Aug 24 2020 - 17:00:02 PDT
