That looks like a .itp file that you can include in your .top file.

To see what a .top should look like, find a small peptide or protein and run it through pdb2gmx to get a .top file. You'll see that there is indeed a section of the .top that is like what you have here. Usually, one then strips that part out into a file like bzp.itp and then in the top one puts "#include 'bzp.itp'" at the appropriate place.

Chris.

-- original message --

Thanks Justin: here is the top:


[ moleculetype ]
; Name            nrexcl
BZP                 2

[ atoms ]


... <snip> ...

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