Error using LigandSwap

[Javier García Marín]

Dear Users and developers,

I'm newer in this community so first of all apologize me if I'll doing some mistake!
I experienced some problems using ligandswap and one of the last files created says:

" Traceback (most recent call last):
File "/panfs/panasas01/chem/jg18729/sire.app/pkgs/sire-2018.2.0/share/Sire/scripts/ligandswap.py", line 248, in <module>
LSRC.run(params)
File "/panfs/panasas01/chem/jg18729/sire.app/lib/python3.5/site-packages/Sire/Tools/__init__.py", line 172, in inner
retval = func()
File "/panfs/panasas01/chem/jg18729/sire.app/lib/python3.5/site-packages/Sire/Tools/LSRC.py", line 2059, in run
(lsrc_system,lsrc_moves) = loadInput()
File "/panfs/panasas01/chem/jg18729/sire.app/lib/python3.5/site-packages/Sire/Tools/LSRC.py", line 1892, in loadInput
(lsrc_system,lsrc_moves) = mergeLSRC(sys0,ligand0_mol, sys1,ligand1_mol, watersys)
File "/panfs/panasas01/chem/jg18729/sire.app/lib/python3.5/site-packages/Sire/Tools/LSRC.py", line 1695, in mergeLSRC
mapping = AtomMCSMatcher(mcs_timeout.val).match(ligand0_mol, PropertyMap(),
Boost.Python.ArgumentError: Python argument types in
AtomMCSMatcher.__init__(AtomMCSMatcher, GeneralUnit)
did not match C++ signature:
__init__(_object*, SireMol::AtomMCSMatcher other)
__init__(_object*, SireMol::AtomMatcher prematcher, SireUnits::Dimension::PhysUnit<0, 0, 1, 0, 0, 0, 0> timeout, bool match_light_atoms, bool verbose)
__init__(_object*, SireMol::AtomMatcher prematcher, bool match_light_atoms, bool verbose)
__init__(_object*, SireUnits::Dimension::PhysUnit<0, 0, 1, 0, 0, 0, 0> timeout, bool match_light_atoms, bool verbose)
__init__(_object*, bool match_light_atoms, bool verbose)
__init__(_object*, SireMol::AtomMatcher prematcher, SireUnits::Dimension::PhysUnit<0, 0, 1, 0, 0, 0, 0> timeout, bool verbose)
__init__(_object*, SireMol::AtomMatcher prematcher, bool verbose)
__init__(_object*, SireUnits::Dimension::PhysUnit<0, 0, 1, 0, 0, 0, 0> timeout, bool verbose)
__init__(_object*, bool verbose)
__init__(_object*) "


On the other hand the log file looks correctly and the last lines are:

"Number of mobile solvent molecules equals 469

Number of fixed (or partially fixed) molecules equals 34925
Merging the two ligand complexes with the water system to create the ligandswap system...

First, mapping the atoms from the first ligand to the atoms of the second...
Starting /panfs/panasas01/chem/jg18729/sire.app/bin/ligandswap: number of threads equals 16"


Does anyone experienced the same problem? I am a little bit confused because i run the same calculations for both ligands using waterswap (and the same input files) and the worked properly.
Have you any tips to breaking through this problem?

Thanks in advance for your time!

Best Regards,

Javier

[Christopher Woods]

  Hi Javier,

The failing code is the maximum common substructure (MCS) matcher that aligns the two ligands. This is not used by waterswap, as there is only one ligand for that method.

The error implies that the AtomMCSMatcher is being passed a GeneralUnit as the timeout parameter, when it should be passed a Time (SireUnits::Dimension::PhysUnit<0, 0, 1, 0, 0, 0, 0> timeout). Are you setting the timeout in the config file?

What is your config file, and which version of Sire are you using?

  Best wishes,

  Christopher

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[Javier García Marín]

Hi Christopher.

I am not using any config file. Since It is the first time that I run this calculations I thought in using default parameters. Should I change something?

I am using the last release for linux 2018_2 compiled in the Bluecrystal Server

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[Christopher Woods]

  Hi Javier,

Could you post the full command line you are using to run ligandswap and send the input files (coordinate / topology) that you are using directly to me by email? I cannot reproduce this error myself using my files, so suspect there is a bug that your input is triggering.

  Best wishes,

  Christopher 

p.s. I’m off on holiday now but will look at this at the end of next week when I am back

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[Javier García Marín]

For sure, Thanks in advance for all your help Christopher 

Best wishes

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[Christopher Woods]

  Hi Javier,

Thanks for your patience while we investigated the problem. The issue was a small change in API introduced in 2018.2.0 that affected the code in LSRC.py. The issue was that we added in a verbosity flag to AtomMCSMatcher, e.g. changing

AtomMCSMatcher(timeout)

to 

AtomMCSMatcher(timeout, verbosity)

We should have set "verbosity" as an optional argument with a default value, e.g.

AtomMCSMatcher(timeout, verbosity=False)

but forgot to do this. We will make this change in the "devel" branch of Sire and will include this with 2018.3.0 which should be out in September.

In the meantime, you can apply a fix to your version of Sire by copying the attached LSRC.py and placing it into $SIRE/lib/python3.5/site-packages/Sire/Tools (where $SIRE is where you have installed Sire, and you should see that this replaces the existing LSRC.py that is in that directory).

There are only a couple of changes in this file, namely;

     if mcs_prematch.val:

         mapping = AtomMCSMatcher( AtomIDMatcher(mcs_prematch.val),

-                                  mcs_timeout.val ).match(ligand0_mol, PropertyMap(),

-                                                          ligand1_mol, PropertyMap())

+                                  mcs_timeout.val, False ).match(ligand0_mol, PropertyMap(),

+                                                                 ligand1_mol, PropertyMap())

     else:

-        mapping = AtomMCSMatcher(mcs_timeout.val).match(ligand0_mol, PropertyMap(), 

-                                                        ligand1_mol, PropertyMap())

+        mapping = AtomMCSMatcher(mcs_timeout.val, False).match(ligand0_mol, PropertyMap(), 

+                                                               ligand1_mol, PropertyMap())

This fixes the problem and should enable your simulations to run. Please let me know if you have any issues.

  Best wishes,

  Christopher

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