[gmx-users] Silly question?

[chris.neale at utoronto.ca]

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> ...