Hi
I am relatively new to mmpbsa calculation and trying to run mmpbsa calculation for protein-ligand complex interaction. I have md trajectory for complex system. I use the following input file
Input file for running PB and GB
&general
endframe=50, keep_files=2,
/
&gb
igb=2, saltcon=0.100,
/
&pb
istrng=0.100,
/
and used the following command: MMPBSA_py -O -i mmpbsa.in -o Final-results.dat -sp complex-solvated.top -cp complex-nowater.top -rp receptor.top -lp ligand.top -y prod.mdcrd
The calculation successfully completed but when I open the file final-results.dat I found that VDWAALS and EEL for protein and complex are nan.
I will highly appreciate you if anyone help me in this regard how to solve this problem
regards
Abdul Wadood, PhD
>Asst. Prof. Dept. of Biochemistry,
>Abdul Wali Khan University Mardan-23200,
>Mardan, Pakistan.
>Office Tel: +92 137 929132
>Mobile : +92 3462623291
>
>
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Received on Thu Nov 13 2014 - 09:00:02 PST
