[gmx-users] Covalent bonds between topology files

[wjallen at vt.edu]

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
...

I will try to decipher this and see what comes of it.  Thankfully, the
renumbering of atoms was not a problem because of the reorder.pl script
available in the user contributions section.  Again, thank you for your reply
Mark, I hope all that I said has made sense.

Cheers,
W. Allen