AMBER Archive (2009)

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

From: Carlos Simmerling (
Date: Mon Mar 30 2009 - 06:30:58 CDT

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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