[gmx-users] patching residues
kaushik.lakkaraju at gmail.com
Wed Jul 18 20:41:39 CEST 2012
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
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.
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