GENESIS with FF19SB

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    • #16382

      tpduy
      Participant

      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 = 0
      `

      Input 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

      ---------------
      Tran Phuoc Duy (チャン フ ズイ)
      Tokyo Institute of Technology 東京工業大学
      School of Life Science and Technology 生命理工学院

    • #16383

      tpduy
      Participant

      [Affected file of the bug]

      genesis-2.0/src/lib/fileio_prmtop.fpp

      ---------------
      Tran Phuoc Duy (チャン フ ズイ)
      Tokyo Institute of Technology 東京工業大学
      School of Life Science and Technology 生命理工学院

    • #16384

      tpduy
      Participant

      The CMAP parameters in AMBER-format input file is not read by GENESIS I guess.
      Maybe additional coding is needed in order to support the new AMBER19SB force field.

      ---------------
      Tran Phuoc Duy (チャン フ ズイ)
      Tokyo Institute of Technology 東京工業大学
      School of Life Science and Technology 生命理工学院

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