[gmx-users] disulphide bonds

[Justin A. Lemkul]

rams rams wrote:
> 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 
> <mailto:gmx-users at gromacs.org>)
>

When do you get this error (i.e., minimization, equilibration, 
production)?  Usually this type of error comes up from a poorly 
minimized/equilibrated structure. 

I agree with Tsjerk that using -merge is the right way to form your 
disulfide, so I assume something else is going wrong during your system 
preparation.  If you'd like to provide details on what you're doing in 
terms of minimization/equilibration, and the contents of the relevant 
.mdp files, we may be able to detect problems.

-Justin

> 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 
> <mailto: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
>     <mailto: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
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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