Thank Justin and Mark, Apologies for not stripping out earlier content from my lazy “Reply” email. It was a slight of hand.
It had crossed my mind to simply make two separate residues as you both suggested. Although I was trying to make most of this interchangeable with the Amber suite (this is an amber forcefield, but unlike my colleagues, I prefer working in Gromacs), in which XLeap can do this. However, with respects to Gromacs, what would happen to the charges? I would essentially have two charge groups if I split them, both not an integer, but when summed as a pair they would be 0 charge. Is this acceptable? Many thanks Anthony Dr Anthony Nash Department of Chemistry University College London On 16/02/2016 16:11, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Mark Abraham" <gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of mark.j.abra...@gmail.com> wrote: >Hi, > >Please start new topics in new emails, rather than confusing the web >archives with replies to digests :-) > >On Tue, Feb 16, 2016 at 5:00 PM Nash, Anthony <a.n...@ucl.ac.uk> 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., >> >> NGLY-MOD-CGLY >> >> | >> NGLY-MOD-CGLY >> >> >> 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). > > >It seems like arranging for your .pdb file to have chain separators that >make gmx pdb2gmx -chainsep whatever -merge interactive would work >smoothly, >and then have specbond mechanism do the crosslink. What can't work is a >single MOD residue, because the early stages of pdb2gmx only know how to >recognize (and handle termini for) an unbranched chain. You might need a >(complete) LYS+ring residue in one chain, and a normal LYS in the other. > >Mark >-- >Gromacs Users mailing list > >* Please search the archive at >http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >posting! > >* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >* For (un)subscribe requests visit >https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.