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> the
first step of creating the top file.
What is 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 <[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 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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