[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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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