[gmx-users] [Fwd: How simulate two peptides in a box?]

gurpreet singh gps.iitm at gmail.com
Mon Jul 2 20:21:16 CEST 2007


 Hello Gromacs users:


I am running a  dimeric protein simulation on Gromacs 3.3 using the force
filed G43a1.


For initially minimizing the hydrogen i did some small minimization and
equilibration in the vacuum by maintaining the restraints
then i added ions and water but in the very first minimization i m getting
the following error


1-4 interaction between 1 and 9 at distance 8.454 which is larger than the
1-4 table size 1.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,


In the log file i am getting :

4 inconsistent shifts check your topology

following is my input file :

title               = 1min in water
define              = -DPOSRES
integrator          = steep
dt                  = 0.001
constraints         = none
nsteps              = 500
nstlist             = 10
rcoulomb            = 1
rlist               = 1
rvdw                = 1.4
ns_type             = grid
coulombtype         = PME
pbc                 = xyz
gen_vel             = no
fourierspacing      = 0.12
pme_order           = 6
ewald_rtol          = 1e-5
optimize_fft        = yes
comm_mode           = angular
emtol               = 100.0
emstep              = 0.01


after adding the ions i have modified the topology file,
please tell me what is the exact reason for this error or what are the
other things i should check in relation to the  error

With regards
Thanks

On 7/2/07, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
>
> Hi Fufeng Liu,
>
> I guess you ran pdb2gmx on the two peptides, where both peptides had
> the same chain identifiers. In that case, pdb2gmx will assume that
> it's one molecule and connect them. Use chain identifiers to indicate
> the different peptides, or build topologies first on separate files
> and combine the peptides later.
>
> Cheers,
>
> Tsjerk
>
> On 7/1/07, Mark Abraham <mark.abraham at anu.edu.au> wrote:
> > Please keep requests for help on the list. That way they're archived for
> > others to use, and other people can raise points of interest.
> >
> > The last sentence here
> >
> http://wiki.gromacs.org/index.php/Errors#1-4_interaction_not_within_cut-off
> > is my suggestion for you :-) Probably, you have only one [molecule]
> > statement for your two molecules, and by chance you included it first so
> > that there was no error message from grompp. If you don't understand why
> > this is a problem, find the relevant section of Chapter 5 of the manual
> -
> > or read the whole lot of that chapter! :-)
> >
> > Mark
> >
> > ---------------------------- Original Message
> ----------------------------
> > Subject: How simulate two peptides in a box?
> > From:    fufengliu at tju.edu.cn
> > Date:    Sun, July 1, 2007 11:09 pm
> > To:      mark.abraham at anu.edu.au
> >
> --------------------------------------------------------------------------
> >
> > Dear Mark:
> >      I'm a graduate student at Tianjin University. I want to simulate
> two
> > peptides
> > in a box using GROMACS software? I followed your suggestion
> >
> > {set up your topologies (suggest one molecule in each of two .itp files)
> > #include them in the .top file, pick a starting configuration for both
> of
> > them in the same structure file, solvate, minimize.}
> >
> > But when I minimized the system, I got the information ¡±1-4 interaction
> > between 83 and 85 at distance 1.862 which is larger than the 1-4 table
> > size 1.000 nm¡±. I checked the topology and found that atom 83 belong to
> > one peptide and the atom 85 the other peptide. That¡¯s to say the two
> > peptides were considered as a peptide. Can you tell me how to do?  I'd
> be
> > very happy and grateful if you could tell me how to do it.
> > Looking forward to your reply.
> >      Best regards.
> >              Fufeng Liu
> >
> >
> >
> >
> >
> > _______________________________________________
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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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