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AuthorPosts
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tpduyParticipantWe 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 -
tpduyParticipant[Affected file of the bug]
genesis-2.0/src/lib/fileio_prmtop.fpp
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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 -
tpduyParticipantThe 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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