[AMBER-Developers] [jonelil.mail.regent.edu: [AMBER] Time numbering problem with constant-pH simulations]

From: David A Case <david.case.rutgers.edu>
Date: Tue, 18 Aug 2020 08:48:20 -0400

Constant pH folks: is there a potential problem with format overflows that we
should fix? See message below, especially the final paragraph.


----- 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
   [cphstats -dio1.mono.cpH.md4.cpin dio1.mono.cpH.md5.cpout name
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 -----

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