[gmx-users] patching residues

Justin Lemkul jalemkul at vt.edu
Wed Jul 18 21:00:10 CEST 2012

On 7/18/12 2:41 PM, kaushik lakkaraju wrote:
> 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.

This is the correct approach, and to my knowledge, the most efficient way that 
Gromacs allows to create non-linear linkages.  pdb2gmx can only create linear 
linkages between residues in a sequence unless specbond.dat is used to create 
branch points in a chain.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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