[gmx-users] disulphide bonds
Justin A. Lemkul
jalemkul at vt.edu
Fri Jun 27 02:49:41 CEST 2008
Please make sure you're including the gmx-users listserv on your
replies. That way, others can weigh in; they may have better ideas than me!
So what you're saying, is if you give: "pdb2gmx -f input.pdb -merge" you
get the error you mentioned before:
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 protonation state.
Option -ignh will ignore all hydrogens in the input.
Is that correct? If so, it seems like someone has been playing with
your .hdb or .rtp files. If you have no H atoms in your input, then
something else very weird is going on...
-Justin
rams rams wrote:
> Dear Justin,
>
> Thanks for your quick replies. But in my starting input pdb I am not
> keeping any of the Hydrogen atoms. I have only the heavy atoms in my
> pdb to start with. All the hydrogens are added by the gromacs. Also I
> didnt face this problem when I am treating the two chains as separate
> one (i.e., if i am not using -merge command ofcourse in that case I
> couldnt see any inter disulphide bonds).
>
> Ram.
>
> On Thu, Jun 26, 2008 at 8:33 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> rams rams wrote:
>
> Hi,
>
> If I use -ignh, that will ignore all the hydrogens in my
> input. And these hydrogens are added by the gromacs.in
> <http://gromacs.in> <http://gromacs.in> the first step of
> creating the top file.
>
>
> What is gromacs.in <http://gromacs.in>? Perhaps it would be best
> if you showed us, step by step, what you are doing (with *exact*
> command lines).
> Using pdb2gmx should be your first step, and using -ignh will
> indeed ignore your hydrogen atoms, but it looks like they're named
> incorrectly anyway, so that might be a good thing. Part of the
> function of pdb2gmx is to add back the appropriate hydrogens
> according to residue templates, so it's irrelevant what you have
> in the input; it's going to be replaced with correct hydrogen
> atoms anyway.
>
> -Justin
>
> Ram.
>
>
> On Thu, Jun 26, 2008 at 3:34 PM, Justin A. Lemkul
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto: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>
> <mailto:gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>> <mailto:gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
>
> <mailto: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>
> <mailto:tsjerkw at gmail.com <mailto:tsjerkw at gmail.com>>
> <mailto:tsjerkw at gmail.com <mailto:tsjerkw at gmail.com>
> <mailto: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>
> <mailto:rams.crux at gmail.com <mailto:rams.crux at gmail.com>>
> <mailto:rams.crux at gmail.com
> <mailto:rams.crux at gmail.com> <mailto: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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> -- ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://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 <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
--
========================================
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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