[gmx-users] crosslinking polypeptide chains

[Nash, Anthony]

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).

I would appreciate any assistance. Many thanks
Anthony



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:

>Hi,
>
>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
>to
>be ready, so there's not a natural list of things people are working on
>for
>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
>>point.
>>
>
>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 :-(.
>
>Mark
>
>I know that the developers are busy, but I am wondering what is in their
>> mind.
>>
>> Thank you.
>>
>> Nicolas
>> --
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