after using -maxwarn 1 command in energy minimization step for ignoring non-zero charge error i got the following error while runing NVT.mdp file through command gmx mdrun -deffnm nvt
Error in user input:
Invalid input values
In option s
Required option was not provided, and the default file ‘topol’ does not
exist or is not accessible.
The following extensions were tried to complete the file name:
.tpr
mdrun is telling you it cannot find the .tpr file you specified and it tries to fall back on the default file name (topol.tpr), which does not exist either. The solution is to (1) ensure that the .tpr file exists in the working directory (in your case, likely grompp failed to produce it) and (2) make sure you haven’t made any typos when specifying the file name.
yes! i don’t have nvt.tpr file should i try the previous step again with command
gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -n index.ndx -o nvt.tpr
grompp will tell you why it failed. Pay attention to all the output in the terminal. Based on your other thread about fractional charges, you probably have lots of issues to sort out before trying to plow ahead. Do not use the -maxwarn option; it is extremely dangerous. Warnings are given when the physics of the calculation is likely to be compromised.
thank you, i also want to know the real reason behind the warning and solve it.
i have checked the topol file, the protein has Heme group inside it in addition to my ligand. system created a separat topol.itp file for Heme and protein. when i checked Heme file, it has a -5.34 charge. after neutralization i think that 0.34 charge left. How i can deal with that