Dan Roe, Viniucius and I are working on this now.
We just want to make sure the change plays nicely with other programs
that also read those files.
Adrian
On 8/18/20 1:14 PM, Jason Swails wrote:
> [External Email]
>
> There shouldn't be a problem with that. The 10.3 field dates back to the
> original ca. 2004 implementation where timescales we're seeing now weren't
> really feasible.
>
> All the best,
> Jason
>
> On Tue, Aug 18, 2020 at 9:02 AM Stephan Schott <schottve.hhu.de> wrote:
>
>> Hi David,
>> I recently stumbled upon this. The formatting for "Time:" in
>> constantph.F90 and constante.F90 is set to f10.3. I guess changing this to
>> 12.3 should do the trick?
>> Cheers,
>>
>>
>> El mar., 18 ago. 2020 a las 14:48, David A Case (<david.case.rutgers.edu>)
>> escribió:
>>
>>> Constant pH folks: is there a potential problem with format overflows
>> that
>>> we
>>> should fix? See message below, especially the final paragraph.
>>>
>>> ...dac
>>>
>>> ----- Forwarded message from Jonee Lillard <jonelil.mail.regent.edu>
>> -----
>>> Date: Sat, 15 Aug 2020 10:31:14 -0400
>>> From: Jonee Lillard <jonelil.mail.regent.edu>
>>> To: amber.ambermd.org
>>> Subject: [AMBER] Time numbering problem with constant-pH simulations
>>>
>>> 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.
>>>
>>> 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
>>>
>>> ----- End forwarded message -----
>>>
>>> _______________________________________________
>>> AMBER-Developers mailing list
>>> AMBER-Developers.ambermd.org
>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber-2Ddevelopers&d=DwIGaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=ElFNNHkXRQC4ElyytToYtj63D0yZ0_Q2FS7GNKFWppE&s=5bDO3zuNK_AVSCEu0enwhuMuzEAD3rdo6bVGYpC8BfQ&e=
>>>
>>
>> --
>> Stephan Schott Verdugo
>> Biochemist
>>
>> Heinrich-Heine-Universitaet Duesseldorf
>> Institut fuer Pharm. und Med. Chemie
>> Universitaetsstr. 1
>> 40225 Duesseldorf
>> Germany
>> _______________________________________________
>> AMBER-Developers mailing list
>> AMBER-Developers.ambermd.org
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber-2Ddevelopers&d=DwIGaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=ElFNNHkXRQC4ElyytToYtj63D0yZ0_Q2FS7GNKFWppE&s=5bDO3zuNK_AVSCEu0enwhuMuzEAD3rdo6bVGYpC8BfQ&e=
>>
>
> --
> Jason M. Swails
> _______________________________________________
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> AMBER-Developers.ambermd.org
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber-2Ddevelopers&d=DwIGaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=ElFNNHkXRQC4ElyytToYtj63D0yZ0_Q2FS7GNKFWppE&s=5bDO3zuNK_AVSCEu0enwhuMuzEAD3rdo6bVGYpC8BfQ&e=
--
Dr. Adrian E. Roitberg
V.T. and Louise Jackson Professor in Chemistry
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Tue Aug 18 2020 - 10:30:03 PDT
