waterswap failed in new version

[B Albert]

Hello, I am trying to run waterswap in the latest SIRE version. But it always failed with following messages

tmp/1> nohup waterswap -c equil.rst -t sol.prmtop -l UNK </dev/null &

[1] 15563

tmp/1> Starting waterswap: number of threads equals 20

Running a waterswap calculation using files sol.prmtop and equil.rst.

The absolute binding free energy of the molecule containing residue UNK will be calculated.

Using parameters:

===============

ligand name == UNK

protein crdfile == equil.rst

protein topfile == sol.prmtop

===============

Loading the protein box system...

Loading from Amber files sol.prmtop / equil.rst...

Loading the molecules from the Amber files "equil.rst" and "sol.prmtop"...

Traceback (most recent call last):

  File "/soft/sire.app/pkgs/sire-2016.3.1/share/Sire/scripts/waterswap.py", line 187, in <module>

    WSRC.run(params)

  File "/soft/sire.app/lib/python3.5/site-packages/Sire/Tools/__init__.py", line 172, in inner

    retval = func()

  File "/soft/sire.app/lib/python3.5/site-packages/Sire/Tools/WSRC.py", line 2750, in run

    (wsrc_system, wsrc_moves) = loadWSRC()

  File "/soft/sire.app/lib/python3.5/site-packages/Sire/Tools/WSRC.py", line 2557, in loadWSRC

    proteinsys = createSystem(protein_topfile.val, protein_crdfile.val, proteinsys_scheme)

  File "/soft/sire.app/lib/python3.5/site-packages/Sire/Tools/AmberLoader.py", line 401, in createSystem

    (molecules, space) = amber.readCrdTop(crd_file, top_file)

UserWarning: Exception 'SireError::incompatible_error' thrown by the thread 'master:main'.

The number of atoms in the crd file (0) does not equal the number of atoms in the top file (61297)!

Thrown from FILE: /home/chris/Sire/corelib/src/libs/SireIO/amber.cpp, LINE: 1927, FUNCTION: boost::tuples::tuple<SireMol::MoleculeGroup, SireBase::PropPtr<SireVol::Space> > SireIO::Amber::readCrdTop(const QString&, const QString&, QString) const

__Backtrace__

(  0) /soft/sire.app/bin/../lib/libSireError.so.2016 ([0x2b3d717cdc9e] ++0x2e)

  -- SireError::getBackTrace()

(  1) /soft/sire.app/bin/../lib/libSireError.so.2016 ([0x2b3d717caab6] ++0x86)

  -- SireError::exception::exception(QString, QString)

/soft/sire.app/bin/../lib/libSireIO.so.2016(+0x57e42) [0x2b3d6ca09e42]

(  3) /soft/sire.app/bin/../lib/libSireIO.so.2016 ([0x2b3d6ca05747] ++0x63f7)

  -- SireIO::Amber::readCrdTop(QString const&, QString const&, QString) const

/soft/sire.app/lib/python3.5/site-packages/Sire/IO/_IO.so(+0x2a6c9) [0x2b3d77d196c9]

(  5) /soft/sire.app/bin/../lib/libboost_python.so ([0x2b3d6d47e57d] ++0x27d)

  -- boost::python::objects::function::call(_object*, _object*) const

/soft/sire.app/bin/../lib/libboost_python.so(+0x27738) [0x2b3d6d47e738]

(  7) /soft/sire.app/bin/../lib/libboost_python.so ([0x2b3d6d471f43] ++0x43)

  -- boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const

/soft/sire.app/lib/python3.5/site-packages/Sire/Error/_Error.so(+0x25d7) [0x2b3d73ee85d7]

(  9) /soft/sire.app/bin/../lib/libboost_python.so ([0x2b3d6d471f28] ++0x28)

  -- boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const

/soft/sire.app/lib/python3.5/site-packages/Sire/Error/_Error.so(+0x2595) [0x2b3d73ee8595]

( 11) /soft/sire.app/bin/../lib/libboost_python.so ([0x2b3d6d471d2d] ++0x2d)

  -- boost::python::handle_exception_impl(boost::function0<void>)

/soft/sire.app/bin/../lib/libboost_python.so(+0x24e09) [0x2b3d6d47be09]

( 13) /soft/sire.app/bin/../lib/libpython3.5m.so.1.0 ([0x2b3d6cfce236] ++0x56)

  -- PyObject_Call

( 14) /soft/sire.app/bin/../lib/libpython3.5m.so.1.0 ([0x2b3d6d0a8314] ++0x66f4)

  -- PyEval_EvalFrameEx

/soft/sire.app/bin/../lib/libpython3.5m.so.1.0(+0x144b49) [0x2b3d6d0abb49]

( 16) /soft/sire.app/bin/../lib/libpython3.5m.so.1.0 ([0x2b3d6d0aadf5] ++0x91d5)

  -- PyEval_EvalFrameEx

( 17) /soft/sire.app/bin/../lib/libpython3.5m.so.1.0 ([0x2b3d6d0ab166] ++0x9546)

  -- PyEval_EvalFrameEx

( 18) /soft/sire.app/bin/../lib/libpython3.5m.so.1.0 ([0x2b3d6d0ab166] ++0x9546)

  -- PyEval_EvalFrameEx

/soft/sire.app/bin/../lib/libpython3.5m.so.1.0(+0x144b49) [0x2b3d6d0abb49]

( 20) /soft/sire.app/bin/../lib/libpython3.5m.so.1.0 ([0x2b3d6d0aadf5] ++0x91d5)

  -- PyEval_EvalFrameEx

/soft/sire.app/bin/../lib/libpython3.5m.so.1.0(+0x144b49) [0x2b3d6d0abb49]

( 22) /soft/sire.app/bin/../lib/libpython3.5m.so.1.0 ([0x2b3d6d0abcd8] ++0x48)

  -- PyEval_EvalCodeEx

( 23) /soft/sire.app/bin/../lib/libpython3.5m.so.1.0 ([0x2b3d6d0abd1b] ++0x3b)

  -- PyEval_EvalCode

( 24) /soft/sire.app/bin/../lib/libpython3.5m.so.1.0 ([0x2b3d6d0d1020] ++0x130)

  -- PyRun_FileExFlags

( 25) /soft/sire.app/bin/../lib/libpython3.5m.so.1.0 ([0x2b3d6d0d2623] ++0x173)

  -- PyRun_SimpleFileExFlags

( 26) /soft/sire.app/bin/../lib/libpython3.5m.so.1.0 ([0x2b3d6d0ed8c7] ++0xca7)

  -- Py_Main

waterswap() [0x40383d]

( 28) /lib64/libc.so.6 ([0x2b3d72c38be5] ++0xf5)

  -- __libc_start_main

( 29) waterswap ([0x402769] ++0x341)

  -- __gxx_personality_v0

__EndTrace__

Exception 'SireError::incompatible_error' thrown by the thread 'master:main'.

The number of atoms in the crd file (0) does not equal the number of atoms in the top file (61297)!

Thrown from FILE: /home/chris/Sire/corelib/src/libs/SireIO/amber.cpp, LINE: 1927, FUNCTION: boost::tuples::tuple<SireMol::MoleculeGroup, SireBase::PropPtr<SireVol::Space> > SireIO::Amber::readCrdTop(const QString&, const QString&, QString) const

[Christopher Woods]

  Hi,

I think that the problem is that the restart file is not an ascii format amber "rst7" file. This format is text, and has a structure similar to;

===

default_name                                                                    

56056  0.2100000E+05

  18.3797826  28.7055373  13.3577900  18.0205478  28.5528170  12.4262715

  18.3357496  29.6981915  13.5389198  17.6757604  28.2934615  13.9533126

  19.6659295  27.9849859  13.3168930  20.0215925  27.9049223  14.3441192

etc.etc.

===

where the first line gives the name of the system, the second line gives the number of atoms and MD timestep, and the rest of the lines give the atomic coordinates and then (optionally) the velocities. More detail about this file format can be found here;

<http://ambermd.org/formats.html#restart>

You can convert your restart file to a rst7 format by using cpptraj in ambertools, e.g. create a file called traj.in file with contents;

=====

trajin equil.rst

trajout equil.rst7

=====

and then run this using

cpptraj -p sol.prmtop < traj.in

This should create a Amber rst7 file called equil.rst7 that you can then input to waterswap.

  Best wishes,

  Christopher

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--

---------------------------------------------------------
Christopher Woods
+44 (0) 7786 264562
http://chryswoods.com