Getting Intermediate structure pdb file during optimisation

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Getting Intermediate structure pdb file during optimisation


Does anyone know how to get an intermediate structure while the optimisation job is still running ?
For me , if the structure isn't optimised and if I stop the job in between , it ends with an error and I do not get the last structure pdb file.

Here is a snippet of the last lines of my input file.
dl-find coords= ${location}/opt_0.c \
result= ${location}/opt_result_0.c \
maxcycle=1500 \
coordinates=hdlc \
residues= $pdbresidues \
active_atoms= $act \
maxene=10000 \
dump=100 \
list_option=full \
optimiser=lbfgs \
maxstep=0.5 \
theory= hybrid : "$hybrid_args"

read_pdb file= rna_solvated_new.pdb coords=dummy.coords
write_pdb file= ${location}/${sys_name_id}.opt.pdb coords=${location}/opt_result_0.c
write_xyz file= ${location}/${sys_name_id} coords=hybrid.${qm_theory}.coords


Is this correct ? or do I have to add anything else?

Thank you.


Since you have list_option=full I think you have a file called which actually is a trajectory of each optimisation step in xyz format.
To get the latest structure in pub format, I generally call use the updated result *.c file and write out the pdb from chemshell prompt. Basically you use the last 2 lines of your script "read_pdb...... " and that will give you the updated pdb of the whole structure from the current step of optimisation and the last line to get the qm part only.

with hdlc_opt module?

Thank you for your reply,

So I was just trying out some calculations using hdlc_opt module. I know that is a depreciated module. But I got good results with the help of that module.
Do you know how can I get a file in that ? Is there any way to get the last structure while using hdlc_opt module?

Waiting for your reply.

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