AMBER Archive (2009)

Subject: Re: [AMBER] .rst file generation problem.

From: Aravind S (
Date: Tue Mar 31 2009 - 03:49:17 CDT

Dear Sir,
I have an other issue that has cropped up when I tried to simulate 227d.pdb.
I was trying to simulate 227d.pdb with the following parameters: there are no constraints involved. I ran the 50 ps simulation with a 10fs time step, temp remaining constant at 300K. By default my ntx=7 and irest=1. My .rst file used was the result got through my previous simulation.
My problem is that the .rst file isnt being generated , only the .mdcrd and the .out files got generated and the .mdcrd files had nothing written on it.
The error in the .out file showed in the results section...
the error read:--- Coordinate resetting (SHAKE) cannot be accomplished,
     deviation is too large
     NITER, NIT, LL, I and J are : 0 2 5 19 21

     Note: This is usually a symptom of some deeper
     problem with the energetics of the system.

I would be highly obliged if somebody could solve this problem of mine.
thank you

----- Original Message -----
From: "Carlos Simmerling" <>
To: "AMBER Mailing List" <>
Sent: Monday, March 30, 2009 5:00:58 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi
Subject: Re: [AMBER] .rst file generation problem.

when restarting after minimization you need to set ntx=1 and irest=0 in your
mdin file.
there are no velocities in minimization so the next step cannot read them.

2009/3/30 Aravind S <>

> Dear Users,
> 1. I had a DNA complex(227.pdb), held fixed with a 500 Kcal/mol restraint
> and minimized for 1000 cycles.
> 2. This was followed by a 25ps MD to warm up the system from 100K to 300K
> with DNA held fixed with a 100 Kcal/mol restraint and a 1fs time step.
> 3. The system was further equilibrated by 25ps of MD at 300K, with the
> restraint on the complex reduced to 50 Kcal/mol and using a 2fs time step.
> 4. Further I ran a 5-step minimization protocol, each of the 1000 steps,
> was then used with the restraint gradually reduced by 5 Kcal/mol
> progressively, while starting with a 25Kcal/mol restraint.
> 5. Finally, the system was created from 100K to 300K using a 10ps MD
> simulation with no harmonic restraints on the complex.
> In this experiment, in the first 4 steps I have successfully generated all
> the output files (.out),(.rst) and (.mdcrd).
> The .rst file that i had got in the 1st step(minimization), I used it in
> the second step and so on...
> PROBLEM: My problem was in the final step wherein I ran the simulation for
> 5000 steps, here the simulation got over in a fraction of a
> second(considering my system to be a Pentium 4) and further on the .rst and
> the .mdcrd files were not generated.
> I opened my output file and an error message was displayed.
> The error message read: FATAL: Could not read velocities from
> dna_wat_4min5.rst
> dna_wat_4min5.rst :- This was the .rst file generated during the final step
> of the 5-step minimization protocol.
> I have attached the input and the output files of the final simulation and
> .rst file of the previous minimization step.
> The command that I used for the final step of simulation is:-
> ./sander -O -i -o dna_wat_mdfiinal.out -p
> dna_wat_prmtop -c dna_wat_4min5.rst -r dna_wat_mdfiinal.rst -x
> dna_wat_mdfiinal.mdcrd -ref dna_wat_4min5.rst
> I would be very thankful if anyone could solve this problem of mine.
> ThankYou
> Aravind S
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