[obasekia]

Good day all, i tried to use implicit sovent model GB for TMD and got an error when i wanted to start production run about unknown parameter for final rmsd. where can i put the final rmsd for implicit solvent model

 

[STEP1] Read Control Parameters

Read_Ctrl_Input> Input Files
prmtopfile = open.prmtop
ambcrdfile = open.crd
rstfile = openeq.rst
ambreffile = closed.crd

Read_Ctrl_Output> Output Files
dcdfile = md_gbsa_target.dcd
rstfile = md_gbsa_target.rst
pdbfile = md_gbsa_target.pdb

Read_Ctrl_Energy> WARNING: “water_model” is not available
Read_Ctrl_Energy> Parameters of Energy Calculations
forcefield = AMBER
switchdist = 23.000 cutoffdist = 25.000
pairlistdist = 28.000 dielec_const = 1.000
debye = 10.000
vdw_force_switch= no
electrostatic = CUTOFF
implicit_solvent= gbsa
gbsa_eps_solvent= 78.50000 gbsa_eps_solute = 1.00000
gbsa_alpha = 1.00000 gbsa_beta = 0.80000
gbsa_gamma = 4.85000 gbsa_salt_cons = 0.20000
gbsa_vdw_offset = 0.09000 gbsa_surf_tens = 0.00500
table_order = 3
table_density = 20.000
water_model = NONE
output_style = GENESIS
dispersion_corr = none
nonb_limiter = no
user def. table = no

End_Ctrlfile_Section> Unknown parameter: [dynamics] “final_rmsd”:
End_Ctrlfile_Section> Stop. rank_no = 0
——————————————————-
Primary job terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
——————————————————-
————————————————————————–
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

Process name: [[50418,1],0]
Exit code: 1
————————————————————————–

[ckobayashi]

Hello,

In atdyn, please use ‘final_value’ instead of ‘final_rmsd’.

There is no description about it in MANUAL and it is confusing, so we will change the description or source code later.

Thank you for your report.

 

Kobayashi