[gmx-users] patching residues

[kaushik lakkaraju]

Hello gromacs users,

I am trying to use pdb2gmx to bring my crystal structure into gromacs
environment. The protein in the crystal has glycosidic linkages. In
charmm, I could attach these carbohydrate structures using PATCH
command.

What is the equivalent of doing this in gromacs?

My initial search of the gromacs manual and forums suggest I build a
new residue that already incorporates this patch and add the new
bonding type to the specbond.dat. However, I am looking to see if
there is a more generic approach; it is likely that there I may need
to attach different types of linkages, in which case, generating a new
residue every time becomes tedious.

Thanks,

Kaushik