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
>>
>> _______________________________________________
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>>
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Received on Sat Aug 22 2020 - 06:30:02 PDT
