Dear amber users,
I am trying to calculate the non-bonded interactions of Cu2+ ions with DNA
around the 5 angstrom of the DNA. In results i am getting positive
van-der-waal energy, i am not able to figure weather there is some mistakes
in my input file or is it something else.
Following are my input commands:-
---------------------------------------------------------------------------------------------------------------
echo "" > op1-ene_nb.txt
for i in {1..5000}
do
echo "parm ../../dna-cu.prmtop
trajin ../tr2-5kfr.nc $i $i
reference ../tr2-5kfr.nc $i $i
strip !(:1-24<:5.0) outprefix dna-cu-op1 nobox
energy nonb_el_vdw .OP1,CU out nonbond_frm.txt nonbond elec vdw
go
quit
" > cppt.in
cpptraj -i cppt.in
tail -n 1 nonbond_frm.txt >> op1-ene_nb.txt
done
rm cppt.in nonbond_frm.txt
--------------------------------------------------------------------------------------------------------------------
Some results of this command is:-
vdw eletro total
1 -0.1009 -638.8666 -638.9676
1 -0.1069 -1101.7432 -1101.8501
1 -0.1213 -1016.8659 -1016.9872
1 -0.1194 -1225.8950 -1226.0144
1 5.8338 -1315.7839 -1309.9501
1 10.3802 -1231.8396 -1221.4594
1 14.5967 -1336.6635 -1322.0668
1 9.9898 -1046.7325 -1036.7427
1 9.2984 -1408.1770 -1398.8786
1 5.5465 -1274.6634 -1269.1169
1 4.6642 -1552.3137 -1547.6495
1 8.3172 -1353.3109 -1344.9936
1 4.9239 -1540.5821 -1535.6582
*-------------------------------------------------*
*With Regards*
*Angad Sharma*
*Research Scholar*
*School of Computational & Integrative Sciences*
*Jawaharlal Nehru University*
*New Delhi 110067, (INDIA)*
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Received on Tue Feb 14 2023 - 06:30:05 PST
