watersawp error

[Faisal Ahmad]

Dear all,
I run waterswap but unfortunately, there is an error after 900 iteration which was set to 1000 iteration as default. The results i got are,

# Free energies
# Bennetts = 12.034569520805391 +/- 0.02734004768729098 kcal mol-1#
# FEP = 12.215717358078578 +/- 18.757356405417596 kcal mol-1#
# TI = 11.965526974988359 +/- 2.196796453961017 kcal mol-1 (quadrature = 11.817384577193447 kcal mol-1)#

Please, can you comment on whether the results I got are reliable to be reported or I need to correct the error to complete the iteration number?


Error after 900 iteration is below,


Running a waterswap calculation using files 1714.prmtop and 1714_prod50.rst.
The absolute binding free energy of the molecule containing residue LIG will be calculated.

Using parameters:
===============
ligand name == LIG
protein crdfile == 1714_prod50.rst
protein topfile == 1714.prmtop
===============

==============================================================
Sending anonymous Sire usage statistics to http://siremol.org.
For more information, see http://siremol.org/analytics
To disable, set the environment variable 'SIRE_DONT_PHONEHOME' to 1
To see the information sent, set the environment variable
SIRE_VERBOSE_PHONEHOME equal to 1. To silence this message, set
the environment variable SIRE_SILENT_PHONEHOME to 1.
==============================================================

Loading the restart file took 4467 ms
Number of iterations to perform: 1000. Number of iterations completed: 900.
Traceback (most recent call last):
File "/home/ngs/miniconda3/share/Sire/scripts/waterswap.py", line 199, in <module>
WSRC.run(params)
File "/home/ngs/miniconda3/lib/python3.7/site-packages/Sire/Tools/__init__.py", line 176, in inner
retval = func()
File "/home/ngs/miniconda3/lib/python3.7/site-packages/Sire/Tools/WSRC.py", line 2956, in run
[res_freenrgs, bound_water_freenrgs, free_water_freenrgs] = Sire.Stream.load(freenrg_components_file)
File "/home/ngs/miniconda3/lib/python3.7/site-packages/Sire/Stream/__init__.py", line 41, in load
header = getDataHeader(data)
UserWarning: Exception 'SireStream::version_error' thrown by the thread 'master:main'.
This data does not appear to have been written by the SireStream::save() function.
Thrown from FILE: /home/sireuser/Sire/corelib/src/libs/SireStream/streamdata.cpp, LINE: 1671, FUNCTION: SireStream::FileHeader SireStream::getDataHeader(const QString&)
__Backtrace__
( 0) /home/ngs/miniconda3/bin/../lib/libSireError.so.2019 ([0x7fb641498c1e] ++0x2e)
-- SireError::getBackTrace()

( 1) /home/ngs/miniconda3/bin/../lib/libSireError.so.2019 ([0x7fb641495a0e] ++0x7e)
-- SireError::exception::exception(QString, QString)

/home/ngs/miniconda3/bin/../lib/libSireStream.so.2019(+0x26ced) [0x7fb6414c9ced]
( 3) /home/ngs/miniconda3/bin/../lib/libSireStream.so.2019 ([0x7fb6414c989f] ++0x2af)
-- SireStream::getDataHeader(QString const&)

/home/ngs/miniconda3/lib/python3.7/site-packages/Sire/Stream/_Stream.so(+0xf170) [0x7fb6283bd170]
( 5) /home/ngs/miniconda3/bin/../lib/libboost_python37.so.1.70.0 ([0x7fb6455474cd] ++0x29d)
-- boost::python::objects::function::call(_object*, _object*) const

/home/ngs/miniconda3/bin/../lib/libboost_python37.so.1.70.0(+0x1f639) [0x7fb645547639]
( 7) /home/ngs/miniconda3/bin/../lib/libboost_python37.so.1.70.0 ([0x7fb64554e30b] ++0x6b)
-- boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const

/home/ngs/miniconda3/lib/python3.7/site-packages/Sire/Error/_Error.so(+0x2a9e) [0x7fb640ee6a9e]
( 9) /home/ngs/miniconda3/bin/../lib/libboost_python37.so.1.70.0 ([0x7fb64554e2da] ++0x3a)
-- boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const

/home/ngs/miniconda3/lib/python3.7/site-packages/Sire/Error/_Error.so(+0x2a5c) [0x7fb640ee6a5c]
( 11) /home/ngs/miniconda3/bin/../lib/libboost_python37.so.1.70.0 ([0x7fb64554e08f] ++0x3f)
-- boost::python::handle_exception_impl(boost::function0<void>)

/home/ngs/miniconda3/bin/../lib/libboost_python37.so.1.70.0(+0x1c6fa) [0x7fb6455446fa]
( 13) /home/ngs/miniconda3/bin/../lib/libpython3.7m.so.1.0 ([0x7fb644f0c005] ++0xc5)
-- _PyObject_FastCallKeywords

/home/ngs/miniconda3/bin/../lib/libpython3.7m.so.1.0(+0x6f071) [0x7fb644e5d071]
( 15) /home/ngs/miniconda3/bin/../lib/libpython3.7m.so.1.0 ([0x7fb644e58808] ++0x4808)
-- _PyEval_EvalFrameDefault

/home/ngs/miniconda3/bin/../lib/libpython3.7m.so.1.0(+0x6de30) [0x7fb644e5be30]
/home/ngs/miniconda3/bin/../lib/libpython3.7m.so.1.0(+0x6f0f6) [0x7fb644e5d0f6]
( 18) /home/ngs/miniconda3/bin/../lib/libpython3.7m.so.1.0 ([0x7fb644e5b10a] ++0x710a)
-- _PyEval_EvalFrameDefault

/home/ngs/miniconda3/bin/../lib/libpython3.7m.so.1.0(+0x6de30) [0x7fb644e5be30]
/home/ngs/miniconda3/bin/../lib/libpython3.7m.so.1.0(+0x6f0f6) [0x7fb644e5d0f6]
( 21) /home/ngs/miniconda3/bin/../lib/libpython3.7m.so.1.0 ([0x7fb644e58808] ++0x4808)
-- _PyEval_EvalFrameDefault

( 22) /home/ngs/miniconda3/bin/../lib/libpython3.7m.so.1.0 ([0x7fb645016284] ++0xac4)
-- _PyEval_EvalCodeWithName

( 23) /home/ngs/miniconda3/bin/../lib/libpython3.7m.so.1.0 ([0x7fb644f0b680] ++0x90)
-- _PyFunction_FastCallKeywords

/home/ngs/miniconda3/bin/../lib/libpython3.7m.so.1.0(+0x6f0f6) [0x7fb644e5d0f6]
( 25) /home/ngs/miniconda3/bin/../lib/libpython3.7m.so.1.0 ([0x7fb644e5b10a] ++0x710a)
-- _PyEval_EvalFrameDefault

( 26) /home/ngs/miniconda3/bin/../lib/libpython3.7m.so.1.0 ([0x7fb645016284] ++0xac4)
-- _PyEval_EvalCodeWithName

( 27) /home/ngs/miniconda3/bin/../lib/libpython3.7m.so.1.0 ([0x7fb64501636f] ++0x3f)
-- PyEval_EvalCodeEx

( 28) /home/ngs/miniconda3/bin/../lib/libpython3.7m.so.1.0 ([0x7fb644ee5abc] ++0x1c)
-- PyEval_EvalCode

( 29) /home/ngs/miniconda3/bin/../lib/libpython3.7m.so.1.0 ([0x7fb644f36037] ++0xb7)
-- PyRun_FileExFlags

( 30) /home/ngs/miniconda3/bin/../lib/libpython3.7m.so.1.0 ([0x7fb644f818b4] ++0xf4)
-- PyRun_SimpleFileExFlags

/home/ngs/miniconda3/bin/../lib/libpython3.7m.so.1.0(+0x1384bf) [0x7fb644f264bf]
( 32) /home/ngs/miniconda3/bin/../lib/libpython3.7m.so.1.0 ([0x7fb644f26749] ++0x39)
-- Py_Main

waterswap(+0x3da8) [0x7fb6456d3da8]
( 34) /lib/x86_64-linux-gnu/libc.so.6 ([0x7fb640815f45] ++0xf5)
-- __libc_start_main

waterswap(+0x467e) [0x7fb6456d467e]
__EndTrace__
Exception 'SireStream::version_error' thrown by the thread 'master:main'.
This data does not appear to have been written by the SireStream::save() function.
Thrown from FILE: /home/sireuser/Sire/corelib/src/libs/SireStream/streamdata.cpp, LINE: 1671, FUNCTION: SireStream::FileHeader SireStream::getDataHeader(const QString&)

[Christopher Woods]

  Hi Faisal,

Thanks for sending your question to us. Your results look really good, as you have strong agreement between the four different methods for estimating the binding free energy (anything within 0.75 kcal mol-1 agreement between Bennetts, FEP, TI and quadrature is great, in my opinion). There is no need to complete the remaining 100 iterations.

The error "This data does not appear to have been written by the SireStream::save() function" suggests that the data file containing residue-based free energy components that is produced by Sire every 100 iterations (freenrg_components.s3) has been corrupted. This can happen if you ran out of disk space (or exceed disk quota) during running the job. This file is very large, and if you run out of disk then it doesn't get written correctly, which is sometimes not detected until a following iteration.

Most people do not use this data, so the freenrg_components.s3 file is not really needed or useful. You can limit the size of this file by changing these options;

energy monitor frequency = 1000  (change from the default of 1000 to 25000)

restart frequency = 10  (change from the default of 10 to 100)

Both of these options will reduce the amount of data and the frequency of writing restarts, which should make save disk space.

  Best wishes,

  Christopher

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---------------------------------------------------------
Christopher Woods
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http://chryswoods.com

[Faisal Ahmad]

Dear 

Christopher Woods

Thanks for sharing such a piece of important views regarding waterswap analysis.

Best Wishes

On Thu, Aug 22, 2019 at 12:19 AM Faisal Ahmad <faisa...@bs.qau.edu.pk> wrote:

To view this discussion on the web visit https://groups.google.com/d/msgid/sire-users/CABNxE02pr3xbBiBQTX7Pwv3pN00p%3D5A1pW8tOxnkPaOm3Zgu%3DQ%40mail.gmail.com.