You will require a .tpr file for many analysis tools. In some cases,
you can get away with a .ndx file. Check g_thistool -h to see what is
mandatory input. You can make a .ndx file if you have a .pdb using
make_ndx -f my.pdb -o my.ndx and then select your groups. If you need
a .tpr file, then you will need a gromacs .top topology file to run
your .pdb and .top through grompp and generate the .tpr. Generating
your .top may be simple if you have a simple system. Try downloading
the amber forcefield that is formatted for gromacs and running your
.pdb through pdb2gmx while selecting that amber ff in order to
generate a .top file.
Note that if you need a .tpr file this is all going to require that
you learn how to use gromacs and will not be completed in one afternoon.
The gromacs manual is quite good.
Chris.
-- original message --
Dear All,
I'm planning to use Gromacs for analysis with Amber trajectory files
( mdcrd, rst files ). And I found a script that converts Amber mdcrd
files to Gromacs-compatible .xtc files. I want to learn that if
Gromacs-compatible .xtc files are enough to perform an analysis using
Gromacs tools ? or Will I have to have some other files for analysis
in Gromacs ? I?m waiting for your suggestions and helps.
Thank you very much for your attention.
Sincerely
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