AMBER Archive (2009)

Subject: Re: [AMBER] "rfree: End of file on unit 5"

From: mathew k varghese (
Date: Mon Mar 30 2009 - 04:57:44 CDT


I think you have to use irest=1 if you are using an .rst file as input coordinate, and ntx=5 if you are using velocity information.


Mathew K Varghese
Research Scholar
School of Pure and Applied Physics
Kottayam, Kerala



--- On Mon, 30/3/09, Remya S R <> wrote:

From: Remya S R <>
Subject: [AMBER] "rfree: End of file on unit 5"
To: "amber" <>
Date: Monday, 30 March, 2009, 11:51 AM


        I was trying to simulate 227d.pdb .First i edited the pdb file , such that it contained only the dna . A 1000 step minimization was carried out by keeping the dna fixed with 500kcal/mol Angstrom. This was then followed by a 25ps MD to warm up the system from 100K to 300K, with the dna fixed with a 100kcal/mol Angstrom restraint and 1fs time step. The system was further equilibrated by 25ps of MD at 300K, with restraint on the dna reduced to 50kcal/mol Angstrom using 2fs time step. A five step minimization protocol, each of 1000 steps was then used with the restraint gradually reduced by 5kcal/mol Angstrom progressively by starting with a 25kcal/mol Angstrom restraint .Till this step , everything went fine.
       Then I ran a 10ps MD simulation to heat the system from 100K to 300K with no restraints on the complex. I used the .rst file from the last minimization step as the coordinate file. This step didn't generate a .rst and .mdcrd file . When I opened the .out file, it had the message
                     "rfree: End of file on unit   5" .

I can't figure out , what went wrong . Please help me fix the problem. I am sending the files used and the command for the last step.

command : ./sander -O -i -o dnafmd.out -p dna_wat.prmtop -c dna_min55.rst -r dnafmd.rst -x dnafmd.mdcrd -ref dna_min55.rst

with regards
-----Inline Attachment Follows-----

AMBER mailing list

      Add more friends to your messenger and enjoy! Go to
AMBER mailing list