empty .top file

[Michelle-Ernst0]

I run a slightly modified version of STx-1.yaml in the Tutorial folder using:
ClayCode builder -f STx1_builder.yaml
This successfully generated the file STx-1_5_3_solv_ions_em.gro along with several others. However, the corresponding STx-1_5_3_solv_ions_em.top file is empty. Is this expected at this stage?

Next, I attempted to perform a d-spacing optimization with:
ClayCode siminp -f STx1_siminp.yaml
This produced two directories with the following contents:
1_EM/
EMjhto38am.gro (empty)
EM.top (empty)
EM.mdp
2_D-SPACE/
2_D-SPACE.mdp
D-SPACE.top (empty)
EM.top (empty)

The empty files don't allow me to run GROMACS.

Builder and siminp input files (renamed from .yaml to .txt):
STx1_builder.txt
STx1_siminp.txt
Compressed output folder:
STx-1.tar.gz

[punkpony]

Hi - thank you for the input.

I opened the .zip file and I can see in the EM:

-rw-rw-r--@ 1 valentina  staff   151K 27 May 15:37 STx-1_5_3_solv_ions_pre_em.top
-rw-rw-r--@ 1 valentina  staff    11K 27 May 15:37 STx-1_5_3_solv_ions_pre_em.mdp
-rw-rw-r--@ 1 valentina  staff   320K 27 May 15:37 STx-1_5_3_solv_ions_pre_em.trr
-rw-rw-r--@ 1 valentina  staff    48K 27 May 15:37 STx-1_5_3_solv_ions_pre_em.log
-rw-rw-r--@ 1 valentina  staff   100K 27 May 15:37 STx-1_5_3_solv_ions_pre_em.gro
-rw-rw-r--@ 1 valentina  staff    20K 27 May 15:37 STx-1_5_3_solv_ions_pre_em.edr
-rw-rw-r--@ 1 valentina  staff    11K 27 May 15:37 STx-1_5_3_solv_ions_em.mdp
-rw-rw-r--@ 1 valentina  staff    27K 27 May 15:37 STx-1_5_3_solv_ions_em.trr
-rw-rw-r--@ 1 valentina  staff    17K 27 May 15:37 STx-1_5_3_solv_ions_em.log
-rw-rw-r--@ 1 valentina  staff   960B 27 May 15:37 STx-1_5_3_solv_ions_em.edr
-rw-rw-r--@ 1 valentina  staff     0B 27 May 15:37 STx-1_5_3_solv_ions_em.top
-rw-------@ 1 valentina  staff   100K 27 May 15:39 STx-1_5_3_solv_ions_em.gro

the system looks fine (except a touch small, the size is x=2.58000 y=2.68980 z=3.50000 nm, which may end up be too small for the non-bonded cut off distances).

the STx-1_5_3_solv_ions_em.top is indeed empty, which is odd. It should be output by gromacs. But it is the same as STx-1_5_3_solv_ions_pre_em.top so should not be a problem per se. @hp115 - can you check this line plz?

Have you tried running the rush.sh that was generated by simpinp?

I am trying to run the script myself, but getting error related to SHELL, which I am quite sure I never saw before. I am calling @hp115 for help.

V