[gmx-users] is there any reasonable way to produce a custom topology?

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Feb 23 09:42:05 CET 2006

Hi Yegor, Mark et al.

Fiddling with the .rtp database is contraindicated in case you have a
distinct ligand, which is not connected to the molecule. In the case of
Yegor, there is need for a connection piece, for which there certainly is a
benefit of having it defined as a building block in the .rtp (especially if
it is not a one-time case). However, that poses other difficulties again.
The format of the .rtp is not that difficult, but there are issues with
regards to the hydrogens, termini and connectivity. Especially the latter
will pose a bit of a problem, I expect, since the -S-CO- bond would not be
simply part in the aa sequence, but has to cross-link two chains together.
It is then also necessary to add two entries in the specbond.dat.

If it is only a one time case, it is possibly better to take a different

Construct the topologies for the two chains to be connected (A and B). Merge
the topologies using the script posted a few days ago. Take off the
hydrogens on the atoms to be used for linking (or change the united force
field atom type) and remove the bonds and angles involved. Draw the region
involving the connection, taking the whole residues on either side of the
-S-CO-. Mark the atoms, bonds, angles and dihedrals (don't forget the
impropers) to be added. Find some parameters for these, which are reasonable
for the X-S-CO-Y connections. Add the atoms, bonds, angles, dihedrals,
improper dihedrals to the appropriate lists. And do add the needed entries
to the [ pairs ] list.

With regards to pdb2gmx.., that's not a particularly friendly program,
especially not from the inside :) But it is documented that you can use
$GMXLIB to point to the databases. Alternatively, you can also put the
modified database files in the working directory, in which case these will
have precedence over the ones in /$GMXDIR/share/top/

Hope it helps,



Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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