Hi,
I am running a very short minimization following the outline of Ross
Walker's tutorial (Simulating a DNA polyA-polyT decamer)
I have protein, DNA, Na+ and water (using AMBER 9 on Irix 64)
my input file is
'Initial minimization w/ position restraints on DNA and zipper, 9.0 cut
&cntrl
ntb = 1,
cut = 9.0,
ntr = 1,
imin = 1,
maxcyc = 1000,
ncyc = 500,
&end
Hold the DNA fixed
100.0
RES 1 40
Hold the protein fixed
100.0
RES 41 154
END
END'
if i load my pdb file in xleap and type desc sys i get
> desc sys
UNIT name:
Head atom: null
Tail atom: null
Contents:
R<DT 1>
R<DT 2>
R<DC 3>
R<DC 4>
R<DT 5>
R<DA 6>
R<DT 7>
R<DG 8>
R<DA 9>
R<DC 10>
R<DT 11>
R<DC 12>
R<DA 13>
R<DT 14>
R<DC 15>
R<DC 16>
R<DA 17>
R<DG 18>
R<DT 19>
R<DT 20>
R<DA 21>
R<DA 22>
R<DA 23>
R<DC 24>
R<DT 25>
R<DG 26>
R<DG 27>
R<DA 28>
R<DT 29>
R<DG 30>
R<DA 31>
R<DG 32>
R<DT 33>
R<DC 34>
R<DA 35>
R<DT 36>
R<DA 37>
R<DG 38>
R<DG 39>
R<DA 40>
R<NLYS 41>
R<ASP 42>
R<PRO 43>
R<ALA 44>
R<ALA 45>
R<LEU 46>
R<LYS 47>
R<ARG 48>
R<ALA 49>
R<ARG 50>
R<ASN 51>
R<THR 52>
R<GLU 53>
R<ALA 54>
R<ALA 55>
R<ARG 56>
R<ARG 57>
R<SER 58>
R<ARG 59>
R<ALA 60>
R<ARG 61>
R<LYS 62>
R<LEU 63>
R<GLN 64>
R<ARG 65>
R<MET 66>
R<LYS 67>
R<GLN 68>
R<LEU 69>
R<GLU 70>
R<ASP 71>
R<LYS 72>
R<VAL 73>
R<GLU 74>
R<GLU 75>
R<LEU 76>
R<LEU 77>
R<SER 78>
R<LYS 79>
R<ASN 80>
R<TYR 81>
R<HIE 82>
R<LEU 83>
R<GLU 84>
R<ASN 85>
R<GLU 86>
R<VAL 87>
R<ALA 88>
R<ARG 89>
R<LEU 90>
R<LYS 91>
R<LYS 92>
R<LEU 93>
R<VAL 94>
R<GLY 95>
R<GLU 96>
R<CARG 97>
R<NMET 98>
R<LYS 99>
R<ASP 100>
R<PRO 101>
R<ALA 102>
R<ALA 103>
R<LEU 104>
R<LYS 105>
R<ARG 106>
R<ALA 107>
R<ARG 108>
R<ASN 109>
R<THR 110>
R<GLU 111>
R<ALA 112>
R<ALA 113>
R<ARG 114>
R<ARG 115>
R<SER 116>
R<ARG 117>
R<ALA 118>
R<ARG 119>
R<LYS 120>
R<LEU 121>
R<GLN 122>
R<ARG 123>
R<MET 124>
R<LYS 125>
R<GLN 126>
R<LEU 127>
R<GLU 128>
R<ASP 129>
R<LYS 130>
R<VAL 131>
R<GLU 132>
R<GLU 133>
R<LEU 134>
R<LEU 135>
R<SER 136>
R<LYS 137>
R<ASN 138>
R<TYR 139>
R<HIE 140>
R<LEU 141>
R<GLU 142>
R<ASN 143>
R<GLU 144>
R<VAL 145>
R<ALA 146>
R<ARG 147>
R<LEU 148>
R<LYS 149>
R<LYS 150>
R<LEU 151>
R<VAL 152>
R<GLY 153>
R<CGLU 154>
The error i get is: 5. REFERENCE ATOM COORDINATES
----- READING GROUP 1; TITLE:
Hold the DNA
fixed
GROUP 1 HAS HARMONIC CONSTRAINTS 100.00000
GRP 1 RES 1 TO 40
rfree: Error decoding variable 2 2 from:
Hold the
this indicates that your input contains
incorrect information
field 2 was supposed to
have a (1=character, 2=integer, 3=decimal) value'
Should change this and use restraintmask function?
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Received on Wed Oct 22 2008 - 05:10:54 PDT
