[gmx-users] How to run pdb2gmx with -ter flag?

Justin Lemkul jalemkul at vt.edu
Thu May 7 13:55:42 CEST 2015

On 5/7/15 4:01 AM, Urszula Uciechowska wrote:
> Hi,
> 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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