On 7/12/12 6:12 AM, [email protected] 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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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