AMBER Archive (2008)

Subject: AMBER: Problems in restrained minimization

From: julliane Yoneda (jullianeyoneda_at_yahoo.com.br)
Date: Wed Jul 23 2008 - 08:08:32 CDT

Dear AMBER users,
 
I need to do a minimization with frozen or restrained atoms in AMBER7.
When I put the following input (with restrained atoms): 
 
minimization
&cntrl
imin=1, ntb=0,
cut=9.0, ntr=1, maxcyc=100000, igb=0,
&end
Restrained atoms
100
RES 2 5
RES 8 29
RES 33
RES 36 61
RES 63
RES 66 84
RES 98
RES 102 110
RES 112 119
RES 122 135
RES 137 141
END
END
 
I have the following error message:
 
 
5. REFERENCE ATOM COORDINATES

----- READING GROUP 1; TITLE:
Restrained atoms

GROUP 1 HAS HARMONIC CONSTRAINTS 100.00000
GRP 1 RES 2 TO 5
GRP 1 RES 8 TO 29
GRP 1 RES 33 TO 33
GRP 1 RES 36 TO 61
GRP 1 RES 63 TO 63
GRP 1 RES 66 TO 84
GRP 1 RES 98 TO 98
GRP 1 RES 102 TO 110
GRP 1 RES 112 TO 119
GRP 1 RES 122 TO 135
GRP 1 RES 137 TO 141
rfree: End of file on unit 5
 
For the following input (frozen atoms): 
 
minimization
&cntrl
imin=1, ntx=1, irest=0, ntrx=1, ntxo=1, ntpr=50, ntf=1, ntb=0,
cut=9.0, nsnb=10, scee=1.2, ntr=0, maxcyc=500, ntmin=1,
ibelly=1,
&end
Belly atoms
RES 1
RES 6 7
RES 30
RES 31 32
RES 34 35
RES 62
RES 64 65
RES 85 97
RES 99 101
RES 111
RES 120 121
RES 136
RES 142 145
END
END
 
I have the following error message:
 
Warning: Although EWALD will work with belly
(for equilibration), it is not strictly correct!
 
LOADING THE BELLY ATOMS AS GROUPS
----- READING GROUP 1; TITLE:
Belly atoms

GRP 1 RES 1 TO 1
GRP 1 RES 6 TO 7
GRP 1 RES 30 TO 30
GRP 1 RES 31 TO 32
GRP 1 RES 34 TO 35
GRP 1 RES 62 TO 62
GRP 1 RES 64 TO 65
GRP 1 RES 85 TO 97
GRP 1 RES 99 TO 101
GRP 1 RES 111 TO 111
GRP 1 RES 120 TO 121
GRP 1 RES 136 TO 136
GRP 1 RES 142 TO 145
rfree: End of file on unit 5
 
I think that the problem is with the format of the input file... I don't know what to do! Could someone help me please?
Thanks;
                          Julliane Yoneda

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