[gmx-users] disulphide bonds

[rams rams]

 Dear Tsjerk,

Thanks for the suggestion but when I use -merge command it says segmentation
error. Let me put the problem in a more elaborated way.

I am running this simulation on insulin. It has two chains "a" and "b" which
are independent fragments but there are two inter disulphide bonds between
the two chains. If I  keep the two chains as a single molecule (as -merge
command does) gromacs could recognize the inter dishlphide bonds but while
running the following error appears:

    396    398  113.3    0.1470   0.2974      0.1470
    398    399   93.1    0.1530   0.4267      0.1530
    399    400   45.5    0.1230   0.1693      0.1230
    399    401   46.5    0.1330   0.1881      0.1330
Step=    2, Dmax= 5.0e-03 nm, Epot= -3.06153e+22 Fmax=         inf, atom= 25
-------------------------------------------------------
Program mdrun, VERSION 3.3.1
Source code file: nsgrid.c, line: 226

Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.

Variable ci has value -2147483648. It should have been within [ 0 .. 1000 ]
Please report this to the mailing list (gmx-users at gromacs.org)

Where as, if I keep these two as separate molecules it couldnt recognize the
two inter disulphide bonds but its running. Now it is adding hydrogens to
the sulhur atoms.

Is there any way to fix this problem ? Is there any way to edit the topology
file to remove the added hydrogen atoms ?

Thanks
Ram.

On Thu, Jun 26, 2008 at 10:26 AM, Tsjerk Wassenaar <tsjerkw at gmail.com>
wrote:

> Hi Ram,
>
> Check the option -merge of pdb2gmx.
>
> Cheers,
>
> Tsjerk
>
> On Thu, Jun 26, 2008 at 6:11 AM, rams rams <rams.crux at gmail.com> wrote:
> > Dear Gromacs users,
> >
> > Is there any way to handle the disulphide bond formed between two
> > independent fragments of a protein ? Precisely it is an inter disulphide
> > bond between two fragments. If I keep the two fragments as separate
> objects
> > while preparing the pdb file (using TER between the two fragments),
> gromacs
> > is not asking for the formation of a disulphide bond. If I keep them as a
> > single object while preparing the input pdb, gromacs could recognize the
> > disulphide bond but while running the energy minimization its complaining
> > that the distances are too close.
> >
> > Is there any way to handle these ? I am also thinking like keep them as
> > separate objects and imposing positional restraints on both the sulphur
> > atoms. Is it all right to do that way ?
> >
> > Please suggest me some thing how to handle these ?
> >
> > Ram.
> >
> > _______________________________________________
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>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
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