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
Received on Tue Aug 25 2020 - 09:00:02 PDT
