Hello, how do I generate a new peptide without a PDB, in a linear conformation from its amino acid sequence? It has been a few years since I did this and I no longer have the input file, but I remember something like GENERATE PEPT 5 ALA ALA ALA etc. Also, once I have that command how do I simulate that peptide, do I just go ahead into the DYNA section or do I need to write a PDB first? I have tried googling it but found nothing.
Thanks a lot!