Hi,
When it comes to diagnosing problems like these, more information is always
better. What was the exact command line you used for cpinutil.py? How was
Amber configured (options, compilers, etc)? Can you send the original
topology you provided to cpinutil.py? Thanks.
-Dan
On Wed, Aug 26, 2020 at 9:04 AM Jonee Lillard <jonelil.mail.regent.edu>
wrote:
> 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
>
> > > >> > > _______________________________________________
>
> > > >> > > 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
>
> >
>
> _______________________________________________
>
> 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 Wed Aug 26 2020 - 07:00:02 PDT
