angle search/find atom error in frag gen
- ozzie787
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8 years 6 months ago #72
by ozzie787
Greetings forum,
I am trying to generate fragments for
the species in my simulation (NVTMC).
When generating fragment files I am getting the following output and error message;My post mortem concludes that the code is searching for an atom that is not part of the fragment outputted as an xyz file, but is somehow part of the array ( frag_list(ifrag,is)%natoms ) used to define the fragment inside the code. If the Clean_Abort() subroutine in participation.f90 at approx line 985 inside the IF statement is disabled, the error also occurs in fragments 5, 9 & 10. In frags 4, 5, 9 and 10 the lookup error occurs during the angle search but uniquely in 10 this also occurs in the dihedral search.
Code compiled and tested using both gfortran and ifort, with the resulting binary giving same error.
Attached are my inputs. Any help, advice or insight on a way forward would be appreciated.
Thank you and every good wish.
I am trying to generate fragments for
the species in my simulation (NVTMC).
When generating fragment files I am getting the following output and error message;
Running Cassandra to generate MCF files...
One of the local ids is zero
This occurred while writing the angle info section
for the ring fragment mcf file
Fragment 4
Species 1
This error occurred in subroutine Write_Ring_Fragment_MCF_Angle_Info.
Fatal Error. Stopping program.Code compiled and tested using both gfortran and ifort, with the resulting binary giving same error.
Attached are my inputs. Any help, advice or insight on a way forward would be appreciated.
Thank you and every good wish.
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- ryangmullen
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8 years 6 months ago #73
by ryangmullen
Hi ozzie787,
The mcfgen.py and library_setup.py scripts parse molecules into fragments composed of either (a) a central atom and all atoms bonded to it, or (b) a single ring and all atoms bonded to a ring atom. So, biphenyl gets parsed into two toluene-like fragments. Each fragment has two atoms in common with adjoining fragments. Neither script, nor Cassandra itself, were designed to handle fused ring structures. For example, if naphthalene were parsed into two fragments according to rule (b) above, the adjoining fragments would have 4 atoms in common. The .pdb you uploaded shows a large biomolecule composed of 6 outer rings that each share 6 atoms with an inner ring fragment. The routines coded in Cassandra won't accommodate such a molecule.
The mcfgen.py and library_setup.py scripts parse molecules into fragments composed of either (a) a central atom and all atoms bonded to it, or (b) a single ring and all atoms bonded to a ring atom. So, biphenyl gets parsed into two toluene-like fragments. Each fragment has two atoms in common with adjoining fragments. Neither script, nor Cassandra itself, were designed to handle fused ring structures. For example, if naphthalene were parsed into two fragments according to rule (b) above, the adjoining fragments would have 4 atoms in common. The .pdb you uploaded shows a large biomolecule composed of 6 outer rings that each share 6 atoms with an inner ring fragment. The routines coded in Cassandra won't accommodate such a molecule.
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