[gmx-users] crosslinking polypeptide chains

Nash, Anthony a.nash at ucl.ac.uk
Tue Feb 16 17:00:01 CET 2016

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 would appreciate any assistance. Many thanks

Dr Anthony Nash
Department of Chemistry
University College London

On 16/02/2016 15:46, "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:

>On Tue, Feb 16, 2016 at 4:07 PM Nicolas Cheron <
>nicolas.cheron.boulot at gmail.com> wrote:
>> Dear all,
>> Is there a place where the planned/hoped new features of Gromacs are
>> listed?
>Kind of. Many times people do some preliminary discussion on Redmine, and
>there's a large amount of stuff people have wished for e.g. at
>http://redmine.gromacs.org/projects/gromacs/roadmap, but also quite a few
>projects around that don't currently have a place there. We do releases
>because it's that time of year, rather than because a feature is thought
>be ready, so there's not a natural list of things people are working on
>that release.
>> I am wondering if there is a chance that EVB, HREX (without the
>> need to use plumed) or new QM/MM interface will be available at some
>I don't know of anybody with short-term plans for these - getting funding
>for software development, and people suited to do it, is always
>challenging, and so a lot of what is available gets channeled into core
>infrastructure, because that pays off for the whole user community. That
>said, there are some forms of HREX you can already do with standard
>GROMACS, and there is infrastructure work going on that would eventually
>permit tools like PLUMED to be implemented in more efficient ways. I know
>that the CPMD team is working on replacing their interface to GROMOS with
>one that will use GROMACS; for that, CPMD will do the driving. The QM-MM
>interface in GROMACS seems not to be interesting for anybody with time to
>work on it :-(.
>I know that the developers are busy, but I am wondering what is in their
>> mind.
>> Thank you.
>> Nicolas
>> --
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