AMBER Archive (2009)
Subject: Re: [AMBER] "rfree: End of file on unit 5"
From: mathew k varghese (mathew_kvarghese_at_yahoo.co.in)
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
--- On Mon, 30/3/09, Remya S R <amm07bi022_at_students.amrita.ac.in> wrote:
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.
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 dna_fmd.in -o dnafmd.out -p dna_wat.prmtop -c dna_min55.rst -r dnafmd.rst -x dnafmd.mdcrd -ref dna_min55.rst
Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/