[gmx-users] more than one protonation per residue with pdb2gmx

Justin A. Lemkul jalemkul at vt.edu
Thu Jul 12 12:15:45 CEST 2012

On 7/12/12 6:12 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
> Hi Justin,
> so you mean that I first have to add the capping groups to my structure
> and then run pdb2gmx with the -ter function?

Yes.  The capping groups (see your force field's .rtp file for available 
entries) are treated as any other residue.  Gromacs will not magically build 
them; they need to be present.

> But how can I add the capping groups to the structure?

You'll have to use some external modeling software for that.



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


More information about the gromacs.org_gmx-users mailing list