[gmx-users] crosslinking polypeptide chains

Nash, Anthony a.nash at ucl.ac.uk
Tue Feb 16 17:22:59 CET 2016

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

Many thanks

Dr Anthony Nash
Department of Chemistry
University College London

On 16/02/2016 16:11, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on
behalf of Mark Abraham" <gromacs.org_gmx-users-bounces at maillist.sys.kth.se
on behalf of mark.j.abraham at gmail.com> wrote:

>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.nash at 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.
>> 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
>It seems like arranging for your .pdb file to have chain separators that
>make gmx pdb2gmx -chainsep whatever -merge interactive would work
>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.
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