The same .top won't work for both a protein and a 3 aa peptide.
Otherwise, you'd better consult your nearest mind-reader, or actually
tell us the error message from grompp. :-)
I only used the same *.mdp file but *.top files where different for
protein and for 3 aa peptide, so it seems that I should use different
*.mdp file. Am I wrong? How could I obtain that *.mdp input for 3 aa
peptide?
Michal
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