Getting Intermediate structure pdb file during optimisation

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helloworld
Getting Intermediate structure pdb file during optimisation

Hi,

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}.QMregion.opt.xyz coords=hybrid.${qm_theory}.coords

*****************************************************************************************************************************************************************************************

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

Thank you.

kakali
Hi,

Hi,
Since you have list_option=full I think you have a file called path.xyz 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.

helloworld
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 path.xyz 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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