[AMBER] Time numbering problem with constant-pH simulations

From: Jonee Lillard <jonelil.mail.regent.edu>
Date: Sat, 15 Aug 2020 10:31:14 -0400

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

*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
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
  [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

AMBER mailing list

Received on Sat Aug 15 2020 - 08:00:02 PDT
Custom Search