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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Received on Thu Aug 28 2003 - 20:53:01 PDT
