Hello,
I have been trying to find the Binding energy for protein DNA
interaction. After preparing the .nc, .prmtop, and .mdcrd files for each of
DNA, protein and complex, I gave the following command
$AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -cp
tttgaa_complex.prmtop -rp tttgaa_prt_2.prmtop -lp tttgaa_2.prmtop -y *.mdcrd
to which it shows the following error:
Error: in read of Coords frame 1 of trajectory DNA.mdcrd.
Error: Could not set up 'DNA.mdcrd' for reading.
Error: Could not set up input trajectory 'DNA.mdcrd'.
Error: Error(s) occurred during execution.
I have stripped WAT AND IONS FROM EACH FILE. ALSO WHAT DOES IT MEAN BY
"Could not set up 'DNA.mdcrd' for reading."
I have attached my DNA.mdcrd file with the mail.
please advise on how to and what to do
Sincerely,
*Manisha*
*Ph.D. Scholar*
Multidisciplinary Centre For Advanced Research and Studies
Jamia Millia Islamia
Delhi-110025
Ph.no: 9518014737
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- application/octet-stream attachment: DNA.mdcrd
Received on Fri Nov 06 2020 - 03:30:04 PST
