Dear all,
I am trying to do MMPBSA calculation on a trajectory with 2:1 binding of
ligands on a receptor. I want to get the energy calculations for all 2
ligands separately and the system with ligands together. To do this, I have
done the following strategy:
1. Created 2 different nc files from the final production.nc by stripping
out 1 ligand each
2. Generated the corresponding prmtop files by stripping atoms using
ante-MMPBSA.py (for dry complex)
But upon running mmpbsa in this system, the following error popped up.
*Preparing trajectories for simulation...
*
*Error: In _MMPBSA_complex.mdcrd.0, expect only 3 or 6 box coords, got 4
*
* Error: Box line=[ 25.896 13.299 29.595 26.322
]
Error: Could not set up '_MMPBSA_complex.mdcrd.0' for
reading. Error:
Could not set up input trajectory '_MMPBSA_complex.mdcrd.0'.
Error: Error(s) occurred during
execution. *
Is it an issue in the generation of files for the purpose of my study? or
could there be any other issue?
The input is :
general
startframe=240000,endframe=250000,interval=5,verbose=2,keep_files=0,
strip_mask=:WAT,28-40
/
&gb
igb=2,saltcon=0.00,surfoff=0.00,surften=0.005,
/
&pb
radiopt=0,inp=1,
&nmode
nmode_igb=0,drms=0.5,dielc=4,maxcyc=10000
/
And the command line:
MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSAall.dat -sp
complex.prmtop -cp complexdry.prmtop -rp rec.prmtop -lp ligand.prmtop -y
production.nc
Regards,
Sruthi Sudhakar
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Received on Fri Jan 14 2022 - 14:00:02 PST
