[gmx-users] disulphide bonds
Justin A. Lemkul
jalemkul at vt.edu
Fri Jun 27 02:00:27 CEST 2008
Justin A. Lemkul wrote:
>
>
> rams rams wrote:
>> 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.
>>
>
> Have you tried -ignh, like the program is suggesting? It looks like
> your hydrogen nomenclature is different than that of the force field
> you're trying to use.
>
> -Justin
>
>> 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
>> <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>>)
>>
>>
>> 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>>> 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>>>
>> 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> | (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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