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/>:
&general
endframe=300, interval=1, verbose=1, strip_mask=:WAT:Na+:Cl-:Mg+:K+:ZN,
/
&gb
igb=8, saltcon=0.15,
/
&decomp
idecomp=4, print_res="1362-1528; 1529-1683; 1-1361; 1817-1856"
dec_verbose=0,
/
Thank you.
Best,
--
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
