[AMBER] MMPBSA Pairwise Internal Energy Issue

From: Pablo Arantes via AMBER <amber.ambermd.org>
Date: Wed, 18 Jan 2023 09:48:02 -0800

Hi Amber team,

I’ve been running MMPBSA Pairwise per-residue free energy decomposition calculations for several systems. We’ve checked all the output files and we have an issue, we don’t have the Internal energy, van der Waals and Electrostatic computed despite setting igb=8. We only have the Polar Salvation and Non-Polar Salvation. Is this always a technical issue for this method? Can you help me address this issue?
The system is protein complex with DNA and RNA.

Follow the command lines and the mmpbsa.in <http://mmpbsa.in/>:

ante-MMPBSA.py -p SYS.prmtop -c com.prmtop -r sele1.prmtop -l sele2.prmtop -s :WAT:Na+:Cl-:Mg+:K+:ZN -n :1529-1683 --radii mbondi3

mpirun -np 32 MMPBSA.py.MPI -O -i mmpbsa.in <http://mmpbsa.in/> -o TadA_RESULTS_MMPBSA.dat -do TadA_DECOMP_MMPBSA.dat -sp SYS.prmtop -cp com.prmtop -rp sele1.prmtop -lp sele2.prmtop -y trajectory.dcd

mmpbsa.in <http://mmpbsa.in/>:

  endframe=300, interval=1, verbose=1, strip_mask=:WAT:Na+:Cl-:Mg+:K+:ZN,
 igb=8, saltcon=0.15,
 idecomp=4, print_res="1362-1528; 1529-1683; 1-1361; 1817-1856"

Thank you.


Pablo Ricardo Arantes
Postdoctoral Research Fellow
PhD in Cell and Molecular Biology - UFRGS
MSc. in Cell and Molecular Biology -  UFRGS
The Palermo Lab
Department of Bioengineering 
University of California Riverside 
225 Materials Science & Engineering
900 University Ave. | Riverside, CA 92521
Email: pabloa.ucr.edu <mailto:pabloa.ucr.edu>
Web: www.palermolab.com <http://www.palermolab.com/>
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Received on Wed Jan 18 2023 - 10:00:03 PST
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