[gmx-users] Fwd: Drug - Enzyme Tutorial

[fulya caglar]

Hi Tsjerk,
  Many thanks for your suggestions.After "grompp -f em.mdp -c trp_b4em.pdb -p trp.top -o trp_em.tpr  " comand there was no warning message.Then I did mdrun ( mdrun -s trp_em.tpr -o trp_em.trr -c trp_b4pr.pdb -g em.log -e em.edr ) and it was finished but
  it gave warning message(Warning: 1-4 interaction between 2100 and 2105 at distance 15.231 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 if not, you should increase table-extension in your mdp file)
And  after second grommp comand (grompp  -f pr.mdp -c trp_b4pr.pdb -p trp.top -o trp_pr.tpr)it gave that error message.
  ----------------------------------------------------------------------------------------
  File input/output error:
trp_b4pr.pdb
----------------------------------------------------------------------------------------
  
I have just checked the log file but there is no different error message.Only this;
   
  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 .. 19488 ]
Please report this to the mailing list (gmx-users at gromacs.org)
   
  ----------------------------------------------------------------------------------------------------------------------------------
  Thanks very much again
  Sincerely
  Fulya

Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
  Hi Fulya,

Did grompp give you any warnings? At what time did the error occur? At
the start of the simulation or later? Could you check the log file for
LINCS warnings, and try to track down the first occurrence? This would
help to be able to say some more than "your system is exploding".

Best,

Tsjerk

On 3/27/07, fulya caglar wrote:
>
>
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> ---------- Forwarded message ----------
> From: fulya caglar 
> To: gmx-users-request at gromacs.org
> Date: Mon, 26 Mar 2007 12:44:18 -0700 (PDT)
> Subject: Drug - Enzyme Tutorial
> Although I could run sucessfully speptide tutorial,while attempting the
> drug-enzyme tutorial I am getting the following error message after the
> first mdrun command ( mdrun -s trp_em.tpr -o trp_em.trr -c trp_b4pr.pdb -g
> em.log –e em.edr);
> -----------------------------------------
>   
>
> ---------------------------------------------------------------------------
>
> I would be very glad to know why I get this type of error. Thanks very
> much.
>
> With thanks
> Sincerely Fulya
>
>
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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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