[gmx-users] crosslinking polypeptide chains

Justin Lemkul jalemkul at vt.edu
Tue Feb 16 17:09:35 CET 2016

On 2/16/16 10:59 AM, Nash, Anthony wrote:
> Hi all,
> When executing pdb2gmx I am getting a fatal error due to dangling bonds. I
> know that it will be down to how I¹ve organised the .pdb file, I¹m just
> lacking in the experience with TERs, -chainsep and -merge to solve this. I
> would appreciate hints/tips/outright-solutions.
> My protein is very simple. It is a proof of concept for forcefield
> parameters I derived myself from QM data (in house software I've
> developed). There are two chains, both are the triplet NGLY-MOD-CGLY. The
> MOD residue is actually a lysine covalently bound to a carbon ring which
> is then covalently bound to the neighbouring chain¹s lysine. It is being
> treaded as one complete residue, MOD. E.g.,
>        |
> Just to reiterate, there is only one instance of the residue MOD, the
> instance has two defined backbones (I.e., backbone as part of each chain).

I don't think you can have one residue across multiple chains.  Split it into 
two parts (e.g. MOD1 and MOD2) and use specbond.dat to connect the two.



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


More information about the gromacs.org_gmx-users mailing list