PRFO TS optimisation

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helloworld
PRFO TS optimisation

Hi ,

I just need a small help with PRFO TS optimisation script.
I am getting an error that says : "DL-FIND ERROR: No residues present in dfl_hdlc_init"
What can I do to correct it ? Is there any issue with my input script keywords here ?

Thank you,
Shreya

******************************************************************************************************************************************************************
Here is my input script:

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

#TS calculation (Input higghest energy fila coordinates from scan)

exec mkdir result
#set location .
set location /scratch/shreya/prfo/result

set control_input_settings [open ${location}/SUMMARY.txt a]
puts $control_input_settings ""

global sys_name_id
set dir .
set sys_name_id rna
source ${dir}/orca.tcl
source ${dir}/hybrid2.tcl

exec cp rna.c ${location}/ts_input.c
exec cp rna_next.c ${location}/ts_input_next.c

#load the connectivity
load_connect_from_psf ${dir}/${sys_name_id}.c ${dir}/rna_solvated.psf
#define force field
set top { top_all36_na.rtf toppar_water_ions.rtf}
set prm ./par_mod.inp
source ${dir}/save_${sys_name_id}.chm

source qmatoms
source act
source pdbresidues

set hybrid_args [ list \
coupling= shift \
groups = $groups \
cutoff=1000.0 \
atom_charges= $charges \
qm_theory=orca : [ list \
hamiltonian=dft \
functional=b3lyp \
executable=/global/orca_4_0_1_2_linux_x86-64_openmpi202/orca \
maxcyc=1500 \
nproc=12 ] \
qm_region= $qmatoms \
debug=no \
mm_theory=dl_poly : [ list \
list_option=medium \
debug=no \
exact_srf=yes \
use_pairlist=no \
mxlist=16000 \
cutoff=1000 \
mxexcl=2000 \
debug_memory=no \
scale14 = { 1.0 1.0 } \
atom_types= $types \
use_charmm_psf=yes \
charmm_psf_file= ${dir}/rna_solvated.psf \
charmm_parameter_file= $prm \
charmm_mass_file= $top ] ] \

dl-find coords= ${location}/ts_input.c \
result= ${location}/ts.opt.c \
coordinates=hdlc \
maxcycle=1500 \
maxene=10000 \
dump=100 \
list_option=full \
maxstep=0.5 \
optimiser=prfo \
active_atoms= $act \
theory=hybrid : "$hybrid_args"

####
# save structure
read_pdb file= rna_solvated_new.pdb
write_pdb file= ${location}/ts.opt.pdb coords= ${location}/ts.opt.c
write_xyz file= ${location}/ts.opt.xyz coords=hybrid.${qm_theory}.coords

tsmode_xyz coords=${location}/ts.opt.c coords2=${location}/ts.opt.next.c \
n=20 delta=1. file=${location}/tsmode_dimer.xyz

tomkeal
tomkeal's picture
PRFO TS optimisation

Hi,

As you have specified coordinates=hdlc, you need to also define the residue list in the dl-find command as described in http://www.cse.scitech.ac.uk/ccg/software/chemshell/manual/hdlc.html#res...

I see you are sourcing a file called pdbresidues, which might contain or generate the required residue information.

Alternatively, you could use a coordinate system which does not require a residue list, such as Cartesian coordinates.

Best wishes,

Tom

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