[gmx-users] How to run pdb2gmx with -ter flag?
jalemkul at vt.edu
Thu May 7 13:55:42 CEST 2015
On 5/7/15 4:01 AM, Urszula Uciechowska wrote:
> Now I have GROMACS v 5.0. What option should I select for -chainsep?
> -chainsep <enum> (id_or_ter)
> Condition in PDB files when a new chain should be started (adding
> termini): id_or_ter, id_and_ter, ter, id, interactive
> Should I change something in my PDB file? This is not clear for me.
> Thank you for your help
You seem to want TER to indicate separate chains, so the default (id_or_ter)
will work, as will ter or interactive, which allows you to specifically choose
which chains are to be separated. The default behavior should have been working
fine without you having to do anything, so if you're getting bonds between
chains, that seems very weird. Make sure you're not just assuming there are
actual bonds from some bad rendering in the visualization software. The
topology is definitive. What you see in VMD et al. is not.
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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