[gmx-users] Build oligosaccharide topology with pdb2gmx

[Elena Lilkova]

Dear GMX community,

I would like to use the CHARMM 36 carbohydrate force field to simulate an
oligosaccharide. I read the pdb2gmx section of the manual, but I am still
wondering how to build the topology for my oligosaccharide.

My first question is can I add in the "residuetypes.dat" residues that are
neither protein, nor DNA, RNA, water, or ions, but say type sugar.

Next, how can I link the individual saccharides. I would like to use two
of the several linkages, that are parameterized in the force field (i.e.
PRES 14aa and PRES 14ab). This means that in both of the two consecutive
saccharides some atoms should be deleted and some partial charges should
be changed.
I now how to do this with the psfgen plugin of vmd, but how am I supposed
to achieve this with pdb2gmx. I should probably make a termini database
file and a special bonds file, right?

Thanks in advance,

Elena Lilkova

elilkova at phys.uni-sofia.bg

PhD student,
Atomic Physics Department,
Faculty of Physics,
University of Sofia "St. Kliment Ohridski"

5 James Bourchier Blvd.
1164 Sofia,
Bulgaria