What version of Amber are you using? I just tested it on my Amber22
compilation and it worked without any issues . For reference, I used the
following command:
$AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -sp cpx_w.prmtop -cp
complex.prmtop -rp receptor.prmtop -lp ligand.prmtop -y md.mdcrd -eo
mmgbsa.csv -prefix mmgbsa_ -o FINAL_RESULTS_MMPBSA.dat -do
FINAL_DECOMP_RESULTS_MMPBSA.dat -deo mmgbsa_decomp.csv
with the following mmpbsa.in file
MMPBSA.py input file
&general
startframe=1, endframe=20000, interval=1,
keep_files=0, netcdf=1,
full_traj=1, strip_mask=:WAT:Cl-:Na+,
/
&gb
igb=2,
/
&decomp
idecomp=1,
/
So maybe you need an update to your AmberTools? I honestly don't think I
have seen that issue before so maybe there is just something wrong with
your compilation.
-Bill
On Wed, Mar 1, 2023 at 10:45 AM Jurica Novak <jurica.novak.biotech.uniri.hr>
wrote:
> Dear Prof. Miller,
>
> Yes, the command ante-MMPBSA works for me, too.
>
> But the problem is when I run the MMPBSA calculation with the command:
> MMPBSA.py -O -i 10_mmpbsa.in -o res_deltaG_01.dat -do decomp_01.dat -sp
> cpx_w.prmtop -cp kompleks.prmtop -rp receptor.prmtop -lp ligand.prmtop -y
> md.mdcrd
> and with the prmtop files generated by ante-MMPBSA.py.
>
> The last line in the _MMPBSA_complex_gb.mdout.0 file then reads
> FATAL: NATOM mismatch in coord and topology files and temporary files
> MMPBSA_complex.pdb, _MMPBSA_receptor.pdb and _MMPBSA_ligand.pdb contain
> only the receptor (all amino acids and HEM, 7705 atoms)
>
> Jurica
>
>
--
Bill Miller III
Assistant Professor of Chemistry
Truman State University
417-549-0952
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Received on Wed Mar 01 2023 - 12:30:03 PST
