[lammps-users] inquiry of advice

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1

Dear LAMMPS users!
We wish to use the LAMMPS code for calculation of the systems
consisting of molecules which fall into the porphyrins family.
But already in an attempt to calculate a molecule of one of
the primary porphyrins � phthalocyanine: C(32)H(18)N(8), we have
faced the problem of construction of the appropriate force field.
   For a molecule of phthalocyanine (file PhC.pdb) two files were
prepared - a topology file (PhC.mdf) and a coordinates file (PhC.car).
In doing so the types of atoms were set to be such as used in
the CVFF force field. But the "msi2lmp" utility which generates
an entrance file of LAMMPS has not found in the cvff.frc file some
combinations of the atoms, namely:

    Unable to find bond data for c= cp
    Unable to find angle data for cp c= n=
    Unable to find angle data for n= c= n=
    Unable to find angle data for c= cp cp
    Unable to find torsion data for n= c= cp cp
    Unable to find oop data for cp c= n= n=
    Unable to find oop data for c= cp cp cp

If ignore this circumstance and to start the LAMMPS code,
it will stop with the error:

    ERROR: incorrect sign arg for dihedral coefficients.

Please, could you give us advice what to do in this case.
Thank you.

G.V.Sin'ko mailto:gevas@…616…

2

Hi,
Look into the corresponding documentation of the dihedral style in LAMMPS to which you are using in your input script. Check you values in data file where some default values is not following the updated LAMMPS allowed values( e.g For dihedral style harmonic n>=0). Replace it with the desired once. For me, i looked up and got the missing data from other force field (ok for my system) and suitably added those in the cvff.frc (comparing the functional form, units and doing some checks) which resulted in data file with no default values generated by msi2lmp. Hope this helps.

Arnab