Dear Amber Users/Developers,
I am doing MD on IHF-DNA complex ( 1ihf.pdb ) with amber 6.0
here is my anal.in:
Analysis file for amino acid residu e interaction with dna & hoh
1 0 0 0 0 1
-1 84.403 84.403 84.403 109.4712206
1 0 0 0 0 1
50.00 2.00 2.00 1.00
0 -10.0 -10.0 -10.0 -10.0 -10.0 -10.0 -10.0 -10.0 -10.0
PDB
ENERGY
ARG54
RES 54
END
seg1
RES 54 55
END
END
STOP
Problem: Seems to me , I can not assign one residue into different
groups.
here is the result : ( part ) for group One , all the result is 0!!
ENERGY CONTRIBUTION BY GROUPS
GROUP BOND ANGLE DIHEDRAL VDW14 EEL14 VDWNB
EELNB HBOND CONSTRAINT TOTAL
1 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.000
2 6.72 13.37 23.30 6.24 -91.92 -16.77
-138.08 0.00 0.00 -197.136
3 970.11 2494.95 3468.66 1258.40 90.50
16499.62-178308.78 0.00 0.00 -153526.547
TOTAL 976.83 2508.32 3491.96 1264.64 -1.42
16482.85-178446.86 0.00 0.00 -153723.688
VDW (N-B + 1-4) INTERACTION ENERGY MATRIX
1 2 3
1 0.000 0.000 0.000
2 0.000 3.421 -27.912
3 0.000 -27.912 17636.430
...
For my research , I want to calculate the energy of different part of
DNA and protein, so , ideally, I will have like:
protein
RES 1 192
END
ARG52
RES 52
END
...
DNA
RES 193 264
END
CENTDNA
RES 206 214
RES 243 251
END
...
but now, I have to separate them into several analin.
Do I have some misunderstanding or something wrong with my analin or ?
Thx!
Best regards,
Lifeng Tian
Dept. of Biochemistry
U . of the Sci. in Philla.
USA
Received on Fri Sep 27 2002 - 15:35:23 PDT
