[gmx-users] disulphide bonds

rams rams rams.crux at gmail.com
Fri Jun 27 02:23:52 CEST 2008 

Hi,

If I use -ignh, that will ignore all the hydrogens in my input. And these
hydrogens are added by the gromacs.in the first step of creating the top
file.

Ram.

On Thu, Jun 26, 2008 at 3:34 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>>    F: +31-30-2537623
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>>
>> ------------------------------------------------------------------------
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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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