AMBER Archive (2009)
Subject: [AMBER] .rst file generation problem.
From: Aravind S (amm07bi007_at_students.amrita.ac.in)
1. I had a DNA complex(227.pdb), held fixed with a 500 Kcal/mol restraint and minimized for 1000 cycles.
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.
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.