[gmx-users] Re: g_rms: Too many iterations in routine JACOBI

[Tsjerk Wassenaar]

Hi,

Maybe good courtesy to sign with a bit more than some initials. It's
so much nicer to have a bit of the impression to know whom you're
talking to.

As for the question, if you would select 'Protein' to extract a part
of your system to a trajectory, this part would likely be the first N
atoms from your system and would therefore correspond one to one with
the first N atoms of your reference structure. Then, running g_rms and
again selecting 'Protein' (or any subset of Protein, e.g. Backbone),
there would be no mismatch between the selection in the trajectory and
the reference. The index file is just a set of numbers. You have to
make sure that some number X points to the same atom in the reference
as it does in the trajectory.

Solutions are: extract the same subset of atoms from your reference to
generate a reference structure matching your trajectory extracted OR
just use the original trajectory with the original reference and use
the index file to select a group in g_rms (or any other tool).

Cheers,

Tsjerk


On Thu, May 8, 2008 at 11:01 AM, minnale <minnale_gnos at rediffmail.com> wrote:
>
>
>
>  Thnaks for your help Tsjerk.
>  One more thing I didnt understand is, if use all same commands except
> choosing options in make_ndx file like " 1 | r 50-80 " generated rmsd.xvg
> without issuing error, but if i use below mentioned commnands showing error,
> which way is correct?
>  Thanks for your appreciation
>
>
>
>  >Hi JS RED,
>
>  >This usually indicates that you have a mismatch between your reference
>  >structure and your trajectory, which is logical as you extracted a
>  >specific set of coordinates from the trajectory, but used an original
>  >(complete) gro file.
>
>  >Hope it helps,
>
>  Tsjerk
>
>  On Thu, May 8, 2008 at 9:18 AM, minnale <minnale_gnos at rediffmail.com>
> wrote:
>  >
>  >
>  >
>  >  Hi all,
>  >  1)I made make_ndx file for my protein because i want to plot rmsd for
>  > specific residues in protein, so I have givenlike this 1 & r 50-80
>  >
>  >  2)Then I have used trjcat -f 1ns.xtc 2ns.xtc 3ns.xtc -n r_50_80.ndx
>  > -settime -o trjout , here I selected
>  >  Protein_&_r_50-80
>  >  this command ran without error,
>  >
>  >  3)After,
>  >  g_rms -f trjout.xtc -pbc -s em_inti.gro -pbc -o rms_3ns
>  >  Select group for least squares fit - 3 c-alpha
>  >  Select group for RMSD calculation - 3  c-alpha
>  >  it showed following error
>  >
>  >  Program g_rms, VERSION 3.3.1
>  >  Source code file: nrjac.c, line: 129
>  >
>  >  Fatal error:
>  >  Error: Too many iterations in routine JACOBI
>  >  I have searched in gmx archives regarding this problem , I found that
>  > mismatch between trjactory and reference structure file, but in my case
> both
>  > are matched atoms
>  >
>  >  Is there any mistake in either selecting options of making index file or
> I
>  > have given wrong option while using g_rms
>  >
>  >  Pls suggest me
>  >  Thanks in advance.
>
>
>
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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