pme_nspline = 4 # order of B-spline in [PME]
pme_max_spacing = 1.0 # max grid spacing
… and so on …
`
What we found error come from:
In AMBER topology file, the FF19SB use CMAP term with include the following %COMMENT line after %FLAG in the CMAP_PARAMETER. The below is an example:
%FLAG CMAP_PARAMETER_01 %COMMENT Gly CMAP %FORMAT(8F9.5)
We recently want to use AMBER19SB with GENESIS version 2.0beta. However, we cannot use with the generated topology file from tleap.
Error from the log file:
Read_Prmtop_Main> error! Please set %FORMAT line for all term. rank_no = 0Input file:
`
[INPUT] prmtopfile = complex.prmtop # input prmtop file ambcrdfile = complex.crd # amber crd file
pdbfile = complex.pdb # pdb file
[OUTPUT] dcdfile = minim.dcd rstfile = minim.rst
[ENERGY] forcefield = AMBER # AMBER force field electrostatic = PME # Particle Mesh Ewald method switchdist = 10.0 # switch distance cutoffdist = 12.0 # cutoff distance
pairlistdist = 14.0 # pair-list distance
pme_nspline = 4 # order of B-spline in [PME] pme_max_spacing = 1.0 # max grid spacing
… and so on … `
What we found error come from:
In AMBER topology file, the FF19SB use CMAP term with include the following %COMMENT line after %FLAG in the CMAP_PARAMETER. The below is an example:
%FLAG CMAP_PARAMETER_01 %COMMENT Gly CMAP %FORMAT(8F9.5)Temporary solution: Delete %COMMENT … line