[gmx-users] Covalent bonds between topology files

[Mark Abraham]

> Thank you for your reply, Mark.  That is what I was afraid of, that I
> would have
> to physically combine the files.  My only problem there is the format of
> the
> topology file that comes from pdb2gmx is slightly different than that
> which
> comes from the PRODRG server.  For example, under the  [ bonds ]  section:
>
> (from pdb2gmx):
> ...
> 5234  5236    2    gb_2
> 5237  5238    2    gb_4
> ...
>
> (and from PRODRG):
> ...
> 5252  5254    1     0.140   334720.0   0.140   334720.0   CAY   NBN
> 5254  5255    1     0.100   374468.0   0.100   374468.0   NBN   HAF
> ...

That's not a problem. The .itp files will have lines like "#define gb_2
<stuff>" which expands to something that resembles the latter examples,
except that the bonded function number is different so the parameter lists
need not match.

Mark