GROMACS modification: No
I did a docking experiments with protein inhibitors and they mutants with some enzymes, and I got very nice results. Now I like to use MD to check stability theses complexes.
Please can anyone help, I need guide line or tutorial for the case.
pdb2gmx handles multiple protein chains natively, as long as each protein is assigned its own chain identifier or is separated by TER. The simulations are functionally no different from a single protein.
Dear Jalemkul, I hope you are fine and salve !!
I want to check if the installation are ok, them I use a file from my docking experiments, done by rosetta programs.
I use lysozyme tutorial with my file and I get:
NOTE 1 [file ions.mdp]:
With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
that with the Verlet scheme, nstlist has no effect on the accuracy of
Setting the LD random seed to -1454148446
Generated 330891 of the 330891 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 330891 of the 330891 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type ‘Protein_chain_E’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_I’
Excluding 2 bonded neighbours molecule type ‘SOL’
NOTE 2 [file topol.top, line 48]:
System has non-zero total charge: 10.000000
Total charge should normally be an integer. See
for discussion on how close it should be to an integer.
Removing all charge groups because cutoff-scheme=Verlet
Analysing residue names:
There are: 253 Protein residues
There are: 11401 Water residues
Number of degrees of freedom in T-Coupling group rest is 79860.00
NOTE 3 [file ions.mdp]:
You are using a plain Coulomb cut-off, which might produce artifacts.
You might want to consider using PME electrostatics.
This run will generate roughly 3 Mb of data
There were 3 notes
I try to continue but I have another problems.
Please can you help me
All of that is normal output. Notes are informational. Warnings and errors are problems.
Please can you check out the file attached ?
em.log (26.8 KB)
Thank’s in advance !!
What am I looking for? The value of Fmax appears a bit high so you should investigate contacts around the atom indicated in the
from last time, I change the version of gromacs, I installed the last one ( 2020.4 ).
I use command " make check " it’s 100% ok.
I did the lysozyme tutorial and ok too.
Please see the log and md files attached to this message.
What am I looking for ?
I try use simulation and MD, to verify or study my docking complex samples,
My sample is complex from docking experiment between protein inhibitor and serine-protease. The contact region understands: residues 28 - 31 for inhibitor and 57, 102, 192,193 and 195 for enzyme.
I also use the umbrella tutorial, but I do not known how to analyses the results, please I need some idea.
All the best
Ricardotipi-wt_HNE_md.log (84.5 KB)