AMBER Archive (2003)

Subject: AMBER: what can't I use ibelly?

From: nie beining (nie_b_at_yahoo.com)
Date: Thu Aug 28 2003 - 14:30:23 CDT

I am a new user of Amber6 with red hat linux platform. I was trying to freeze protein while allowing water molecules and ions to move for equilibration. I used ibelly flag in PIN file and sander gave me this message in MDOUT file and quit calculation
"Warning: Although EWALD will work with belly

(for equilibration), it is not strictly correct!

 

LOADING THE BELLY ATOMS AS GROUPS

----- READING GROUP 1; TITLE:

GRP 1 RES 126 TO 4906

rfree: End of file on unit 5"

 

And inputs in PIN file are:

"&cntrl

imin=0, ncyc=50, maxcyc=1000, ntx=1,

ntt=1, temp0=300.0, tautp=0.2, irest=0,

ntb=2, ntf=2, ntc=2,

ntp=1, pres0=1.0, ibelly=1,

ntr=0, ntrx=1, cut=12.0,

dt=0.002, ig=77751, nstlim=100,

ntpr=1, ntwx=1, ntwe=1

&end

RES 126 4906

END

END"

I don't understand the error message. Please explain. Thanks!

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