Re: [gmx-users] disulphide bonds

Justin A. Lemkul Thu, 26 Jun 2008 17:01:04 -0700


Justin A. Lemkul wrote:



rams rams wrote:

Hi,
The merge command did worked well in creating the disulphide bondsbut with that I ran into some other problem. Is there any thing elseto add along with the -merge ?
Since I have two independent chains, its asking for the n-terminusand c-terminus twice. I am giving them as NH3+ and COO- in both thecases. Since I like to have them as such. Now with the merge command,its complaining like the following:
Fatal Error:
Atom H1 in residue PHE 22 not found in rtp entry with 17 atoms
             while sorting atoms. Maybe different protonation state.
Remove this hydrogen or choose a different protonationstate.
             Option -ignh will ignore all hydrogens in the input.

Have you tried -ignh, like the program is suggesting? It looks likeyour hydrogen nomenclature is different than that of the force fieldyou're trying to use.


-Justin

My PHE22 is the starting residue of my second chain and my firstchain ends with Aspargine. Though its creating the _pwi2MM.pdb filebut nothing I can find in _pwi.top file.


Can some one suggest me something to fix this ?

Thanks and Regards,
Ram.

On Thu, Jun 26, 2008 at 3:34 PM, Justin A. Lemkul <[EMAIL PROTECTED]<mailto:[EMAIL PROTECTED]>> 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@gromacs.org
        <mailto:gmx-users@gromacs.org> <mailto:gmx-users@gromacs.org
        <mailto:gmx-users@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
        <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
        <mailto:[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>> wrote:

           Hi Ram,

           Check the option -merge of pdb2gmx.

           Cheers,

           Tsjerk

           On Thu, Jun 26, 2008 at 6:11 AM, rams rams
        <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
           <mailto:[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>>
        wrote:
           > Dear Gromacs users,
           >
           > Is there any way to handle the disulphide bond formed
        between two

> independent fragments of a protein ? Precisely it is aninter

           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 energyminimization 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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    --     ========================================

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

    ========================================


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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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Re: [gmx-users] disulphide bonds

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