Hi,
I am trying to run a MD simulation of a protein-ligand complex in a cluster.
The npt run is complete and the log file doesn't show any error.
Next the grompp also runs, without throwing any error.
But when I try 'gmx mdrun -v -deffnm md', it says md.tpr doesn't exist. This file was to be generated in the grompp step. But it didn't. Any suggestions how to resolve this?
Thanks
Perhaps your *.mdp files could be missing, there a total of 5 *.mdp files (em, em_real, md, npt, nvt). Also you need to do certain editing in several files like, topol.top and in some of these *.mdp files. Hope it helps, all the best.
gmx grompp -f md.mdp -c npt.gro -t npt.cpt -n index_protein_ligand.ndx -p topol.top -o md_200ns.tpr
gmx mdrun -v -deffnm md_200ns
These are the commands I used.
Your tpr file is named md_200ns.tpr
Try using the command
gmx mdrun -v -deffnm md_200ns
Good luck...
Perhaps your *.mdp files could be missing, there a total of 5 *.mdp files (em, em_real, md, npt, nvt). Also you need to do certain editing in several files like, topol.top and in some of these *.mdp files. Hope it helps, all the best.
Thank you all for your answers. I was running the NVT, NPT and MD in a cluster which has gromacs 4.6 installed.
I generated the initial files til energy minimization in my computer, which has 5.1.4 installed.
The problem arised because of difference in versions. I installed 4.6 on my computer and all is good now.
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