AMBER Archive (2009)

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

From: Aravind S (amm07bi007_at_students.amrita.ac.in)
Date: Mon Mar 30 2009 - 01:32:12 CDT

Dear Users,

1. I had a DNA complex(227d.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 dna_wat_mdfiinal.in -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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