Samuele Di Cristofano
Hi everyone,
I’m trying to perform an Alanine Scanning calculation on a Protein - Ligand system, but I’m encountering the following error:
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No protocol specified
[INFO ] Starting
[INFO ] Command-line
gmx_MMPBSA -O -i mmpbsa.in -cs MD.tpr -cp topol.top -ci index.all.ndx -cg 1 13 -ct traj.xtc
[WARNING] protein_forcefield and ligand_forcefield variables are deprecate since version 1.4.1 and will be remove in the next version. Please, use forcefield instead.
[WARNING] entropy_seg variable is deprecate since version 1.4.2 and will be remove in v1.5.0. Please, use ie_segment instead.
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /data/sam/bioHP3/sw/amber20/bin/cpptraj
[INFO ] tleap found! Using /data/sam/bioHP3/sw/amber20/bin/tleap
[INFO ] parmchk2 found! Using /data/sam/bioHP3/sw/amber20/bin/parmchk2
[INFO ] sander found! Using /data/sam/bioHP3/sw/amber20/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /data/bioHP3/sw/gromacs_2020.4/installation/bin/gmx
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER Topologies from GROMACS files...
[INFO ] Checking gmxMMPBSA data folder exists in Amber data...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Normal Complex: Saving group 1_13 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Complex: Saving group 1 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal ligand: Saving group 13 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO ] Building Normal Complex Amber Topology...
[INFO ] Writing Normal Complex Amber Topology...
[INFO ] No Receptor topology files was defined. Using ST approach...
[INFO ] Building AMBER Receptor Topology from Complex...
[INFO ] No Ligand Topology files was defined. Using ST approach...
[INFO ] Building AMBER Ligand Topology from Complex...
[INFO ] Building Mutant Complex Topology...
[INFO ] Mutating THR by ALA
[INFO ] Setting intdiel = indi = intdiel_polar = 3 for Alanine scanning
[INFO ] Detecting mutation in Receptor. Building Mutant Receptor Topology...
[INFO ] Cleaning normal complex trajectories...
[INFO ] Building AMBER Topologies from GROMACS files...Done.
[INFO ] Loading and checking parameter files for compatibility...
Preparing trajectories for simulation...
Mutating trajectories...
50 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning GB calculations with /data/sam/bioHP3/sw/amber20/bin/sander
calculating complex contribution...
calculating receptor contribution...
calculating ligand contribution...
Running calculations on mutant system...
Beginning GB calculations with /data/sam/bioHP3/sw/amber20/bin/sander
calculating complex contribution...
calculating receptor contribution...
no mutation found in ligand; using unmutated files
File "/home/domenico/anaconda3/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/domenico/anaconda3/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 107, in gmxmmpbsa
app.parse_output_files()
File "/home/domenico/anaconda3/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 1076, in parse_output_files
outclass[i](self.pre + 'mutant_' + basename[i] % 'complex',
File "/home/domenico/anaconda3/lib/python3.9/site-packages/GMXMMPBSA/amber_outputs.py", line 696, in __init__
AmberOutput._read(self)
File "/home/domenico/anaconda3/lib/python3.9/site-packages/GMXMMPBSA/amber_outputs.py", line 341, in _read
self._get_energies(output_file)
File "/home/domenico/anaconda3/lib/python3.9/site-packages/GMXMMPBSA/amber_outputs.py", line 723, in _get_energies
self.data['VDWAALS'].append(float(words[2]))
ValueError: could not convert string to float: '*************'
Error occured on rank 0.
Exiting. All files have been retained.
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My “mmpbsa.in” file is the following:
&general
sys_name="Protein_LIG in water_CAS",
startframe=1, endframe=100, interval=2, verbose=2,
forcefields="oldff/leaprc.ff14SB,leaprc.gaff", PBRadii=4,
/
&gb
igb=8, saltcon=0,
/
&alanine_scanning
mutant='ALA', mutant_res="A:173", cas_intdiel=1
/
The input files should be correct and the PBCs correctly treated, as I’m able to calculate MM/PBSA and Per-Residue Decomposition Energy with no problems.
This error appear only when I try to mutate a Threonine to an Alanine, otherwise the program works well with other residue type.
I suspect that the problem arise in the mutated receptor (here attached), in fact the .pdb files is clearly corrupted from the point of mutation until the end of the protein (res. 174-240).
Any comments or suggestion are welcome.
Thanks in advance,
Samuele
Mario Sergio Valdes
Samuele Di Cristofano
Mario Sergio Valdes
marioe911116
- The residue number is incorrect. It had already been previously reported (resolved for version 1.5.0)
- The mutation of residues like THR generates an inconsistent mutant structure (Also in version 1.5.0)