Hi Pablo,
This is definitely not typical of MMPBSA.py. I would expect to see no
values for the internal energies for a protein-DNA complex because they
should exactly cancel for the DELTA energies. However, I would expect to
see the vdW and electrostatic energy terms in the output files. Do you see
vdW and electrostatic energies in the regular energy output files, or are
they only missing from the decomp output files? Can you send an excerpt
from the output files maybe so we can see them?
-Bill
On Wed, Jan 18, 2023 at 11:48 AM Pablo Arantes via AMBER <amber.ambermd.org>
wrote:
> 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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>
--
Bill Miller III
Assistant Professor of Chemistry
Truman State University
417-549-0952
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Received on Thu Jan 19 2023 - 10:00:02 PST
