[gmx-users] disulphide bonds
rams rams
rams.crux at gmail.com
Fri Jun 27 01:47:29 CEST 2008
Hi,
The merge command did worked well in creating the disulphide bonds but with
that I ran into some other problem. Is there any thing else to add along
with the -merge ?
Since I have two independent chains, its asking for the n-terminus and
c-terminus twice. I am giving them as NH3+ and COO- in both the cases. 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 protonation state.
Option -ignh will ignore all hydrogens in the input.
My PHE22 is the starting residue of my second chain and my first chain ends
with Aspargine. Though its creating the _pwi2MM.pdb file but 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 <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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