I want to run an MD simulation for Protein-ligand complex and following Gromacs tutorial of Justin Lemkul Department of Biochemistry, Virginia Tech. I have successfully generated "jz4.gro" and "drg.itp." and other file. But not generate a nvt.tpr file.
when write this command i,e mdrun -deffnm nvt
Reading file nvt.tpr, VERSION 4.5.5 (single precision)
Starting 2 threads
Making 1D domain decomposition 2 x 1 x 1
starting mdrun 'Protein in water'
50000 steps, 100.0 ps.
some time later this warning appears
Step 9092, time 18.184 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.030250, max 0.645110 (between atoms 2564 and 2563)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
2562 2560 41.2 0.1391 0.1834 0.1390
2569 2562 33.8 0.1391 0.1708 0.1390
2563 2562 86.0 0.1481 0.2060 0.1480
2567 2563 35.8 0.1480 0.1413 0.1480
2564 2563 86.5 0.1331 0.2188 0.1330
2565 2564 50.3 0.1230 0.2012 0.1230
2567 2566 90.2 0.1530 0.1789 0.1530
2568 2567 63.9 0.1430 0.1736 0.1430
Wrote pdb files with previous and current coordinates
Step 9093, time 18.186 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.125133, max 2.551737 (between atoms 2567 and 2563)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
2562 2560 86.0 0.1834 0.3064 0.1390
2569 2562 126.5 0.1708 0.2158 0.1390
2563 2562 125.2 0.2060 0.4370 0.1480
2567 2563 45.6 0.1413 0.5257 0.1480
2564 2563 149.1 0.2188 0.4058 0.1330
2566 2564 137.4 0.1526 0.1483 0.1390
2565 2564 83.8 0.2012 0.3080 0.1230
2567 2566 32.5 0.1789 0.3267 0.1530
2568 2567 35.5 0.1736 0.2955 0.1430
2570 2569 46.1 0.1514 0.0888 0.1330
2571 2570 38.1 0.1586 0.1912 0.1530
Wrote pdb files with previous and current coordinate
step 9095: Water molecule starting at atom 26335 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Segmentation fault (core dumped).
Clearly nvt.tpr was generated, because you're running the simulation. It has become unstable, which suggests that either (1) your system was insufficiently minimized, (2) your .mdp settings are incorrect, and/or (3) the ligand topology is flawed.
Clearly nvt.tpr was generated, because you're running the simulation. It has become unstable, which suggests that either (1) your system was insufficiently minimized, (2) your .mdp settings are incorrect, and/or (3) the ligand topology is flawed.
A .tpr file is generated by grompp, which needs a .mdp (parameter file) and some conformational/topological information (.gro, .top files) as inputs. The above error seems to suggest that the initial model you have is behaving in an unphysical manner, that is, 1) there may be atoms/particles overlapping, causing a massive increase in energy, 2) the configuration of the model is not in an energetically minimized state. Try running some position restraint simulations before the nvt run.
Thank you sir.
One silly question i have asked, how to overcome this factor i,e atoms/particles overlapping, causing a massive increase in energy and the model is not in an energetically minimized state
If energy minimization does not converge adequately, then your starting coordinates are poorly prepared. In creating protein-ligand complexes, it is easy to mess up the coordinates if you are not careful.
I am trying to simulate a complex (protein + ligand) complex obtained from Autodock software. My complex contains 1 protein + ligand. Using this complex im trying to follow justin tutorial.
I have seprated protein and ligand from the complex and make two files:
1.protein.pdb
2. ligand.pdb
Then apply pdb2gmx command on protein.pdb file to generate topology file .top and .gro .
Generate ligand topologies using PRODRG tool and then make additions in the .gro file and .top file of pdb as given in the tutorial.
After that i have done Editconf and created dodecahedron box.
Then i have use grompp command to assemble a .tpr file, using any .mdp file for running energy minimization.
How to known energy minimization does not converge adequately?
For generating .tpr file you can use grompp. But if you don't have .tpr file how did you run the simulation? Is the possible that you had an old .tpr file and you are running simulation using that?
Hello Sandip Dolui,
your nvt.tpr file is already generated and you found warning message in simulation step. So, just open your .mdp file and go to the Bond parameters step, where you see constraints = all-bonds. Try to change all-bonds to h-bonds (constraints = h-bonds). Now, run your simulation step (mdrun).
I hope it will help you
If u want to use charmm force field, then i will help u for successfully run of protein-ligand simulation. I also getting same error for tutorial follow up. Most probable problem is, ligand topology not generated properly.
@Sachin Patel, I had changed all-bonds to h-bonds and ran the simulation step and it worked but I wonder will this bring any difference in my results? Can I go ahead with my analysis?
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