Hello,
I want to use the final structure of gromacs after 100ns to run a GaMD simulation with amber software. So，I should turn the gromacs' top and gro files into amber's parm and rst files?
I searched on the Internet that parmed can be transferred, but our server's parmed software cannot be used.
Is there any other way to turn them?
Thank.
Hi,
it has been a while, since the question was posed... For completeness, here a quick answer to the problem.
AmberTools comes with ParmEd, which can convert topology files (though I am unsure if there are limitations. Maybe ask to the amber mailing list).
Start parmed, and convert the topologies with the following commands:
```
gromber TOPOL.top COORD.gro topdir /path/to/your/itp/files
outparm TOPOL.prm7 COORD.rst7
quit
```
gromber loads a GROMACS topology (TOPOL.top) and the coordinates (COORDS.gro). To resolve the #include statements you need to provide the location of the *.itp files (/path/to/your/itp/files). If you use any of the default force fields that path should be `$GROMACS_DIR/share/gromacs/top`.
outparm writes the converted topology and coordinates.
Cheers!
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