# Experiment wit complexes proteins **URL:** \ **Category:** User discussions\ **Created:** [December 15, 2020, 3:51pm UTC](https://gromacs.bioexcel.eu/t/experiment-wit-complexes-proteins/1276 "2020-12-15T15:51:08Z")\ **Posts on this page:** 7\ **Page:** 1
**Author:** ![torquato](https://avatars.discourse-cdn.com/v4/letter/t/8baadc/32.png) [@torquato](https://gromacs.bioexcel.eu/u/torquato)\ **Post date:** [December 15, 2020, 3:51pm UTC](https://gromacs.bioexcel.eu/t/experiment-wit-complexes-proteins/1276/1 "2020-12-15T15:51:08Z")
GROMACS version:2020.3 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. Thank’s Ricardo ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [December 16, 2020, 2:01am UTC](https://gromacs.bioexcel.eu/t/experiment-wit-complexes-proteins/1276/2 "2020-12-16T02:01:46Z")
`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. ---
**Author:** ![torquato](https://avatars.discourse-cdn.com/v4/letter/t/8baadc/32.png) [@torquato](https://gromacs.bioexcel.eu/u/torquato)\ **Post date:** [December 24, 2020, 6:54pm UTC](https://gromacs.bioexcel.eu/t/experiment-wit-complexes-proteins/1276/3 "2020-12-24T18:54:11Z")
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 your simulation. 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 [http://www.gromacs.org/Documentation/Floating\_Point\_Arithmetic](http://www.gromacs.org/Documentation/Floating_Point_Arithmetic) 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 Analysing Protein… 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 Thank’s ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [December 29, 2020, 2:39am UTC](https://gromacs.bioexcel.eu/t/experiment-wit-complexes-proteins/1276/4 "2020-12-29T02:39:19Z")
All of that is normal output. Notes are informational. Warnings and errors are problems. ---
**Author:** ![torquato](https://avatars.discourse-cdn.com/v4/letter/t/8baadc/32.png) [@torquato](https://gromacs.bioexcel.eu/u/torquato)\ **Post date:** [January 3, 2021, 12:30am UTC](https://gromacs.bioexcel.eu/t/experiment-wit-complexes-proteins/1276/5 "2021-01-03T00:30:10Z")
Please can you check out the file attached ? [em.log](https://gromacs.bioexcel.eu/uploads/short-url/fb1IX64qArTHXoRBZVwzfX8iehS.log) (26.8 KB) Thank’s in advance !! Ricardo ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [January 5, 2021, 3:50pm UTC](https://gromacs.bioexcel.eu/t/experiment-wit-complexes-proteins/1276/6 "2021-01-05T15:50:01Z")
What am I looking for? The value of Fmax appears a bit high so you should investigate contacts around the atom indicated in the `.log` file. ---
**Author:** ![torquato](https://avatars.discourse-cdn.com/v4/letter/t/8baadc/32.png) [@torquato](https://gromacs.bioexcel.eu/u/torquato)\ **Post date:** [January 5, 2021, 6:26pm UTC](https://gromacs.bioexcel.eu/t/experiment-wit-complexes-proteins/1276/7 "2021-01-05T18:26:00Z")
Hi, jalemkul. 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 Ricardo[tipi-wt\_HNE\_md.log](https://gromacs.bioexcel.eu/uploads/short-url/uPtoxMLWjIQ8Kgj6t4UcJIHEekW.log) (84.5 KB)