I am working on molecular dynamics simulation in Gromacs. The output of the pdb2gmx is not working properly: only the .itp file and the .top file generate, not the .pdb/.gro files (output files).
There is a manual for using pdb2gmx, follow this link:
http://manual.gromacs.org/online/pdb2gmx.html
For *.pdb file you need -q option and for *.gro you will need -o option.
If you are already using this manual, then you can provide a log output file, so we can have a look and maybe help you.
what Mr. Kamberaj pointed is a good source. You can find a lot more in the link below. In general "pdb2gmx" should not create any problem. log file would give you a lot information. I hope you can fix it in no time. If persists let us know.
http://www.gromacs.org/Documentation/Tutorials
or
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/
Did you get any error after you ran the command? if yes what was the error?
By using GROMACS-2019, the 'gmx pdb2gmx' command generates an error in user input:
Invalid command-line options. In command-line option -f
File '1AKI_clean.pdb' does not exist or is not accessible.
The file could not be opened.
It did not happen with GROMACS-2018.... Does anybody may help me with this issue? Should I have to return to GROMACS-2018?
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