Dear amber users,
I had been trying to calculate the energy of a DNA duplex using the ANAL
module of AMBER. But i am doubtful of the input file I am using for the
calculation.
Itwould be nice if somebody can tell whether the below input files is
correct.
Below is the input file used for calculating the energy
********************************************************
Energy of the duplex
1 0 0 0 0 1
0 0.0 0.0 0.0 0.0
1 0 1 0 50 0
12.0 2.0 1.2 1.0
0 0.0 0.0 0.0 0.0 0.0 0. 0. 0. 0.
ENERGY
Ter residues
ATOM 1 64 395 461 462 519 820 880
END
BASE GROUP
ATOM 77 91 110 124 143 157 176 190 209 223
ATOM 242 256 275 289 308 322 341 355 374 388
ATOM 532 543 562 573 592 603 622 633 652 663
ATOM 682 693 712 723 742 753 772 783 802 813
END
Phosgroup
ATOM 65 68 97 101 130 134 163 167 196 200 229 233
ATOM 262 266 295 299 328 332 361 365 394 394
ATOM 520 523 549 553 579 583 609 613 639 643 669 673
ATOM 699 703 729 733 759 763 789 793 819 819
END
END
STOP
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
A part of the output files showing the input parameters is given below
---------------------------------------------------------------
Amber 5.0 ANAL: Static Analysis for Energy/Structure UCSF 1997
---------------------------------------------------------------
1. RESOURCE USE:
Memory Use Allocated Used
Real 500000 27974
Integer 800000 35636 (static)
| Max Nonbonded Pairs: 1528728 packed 2 to a machine word
2. DATA CONTROL:
Rev A Generic Anal.in for Gross Error Checking. Assumes formatted files
NTX = 1 NTXO = 0 NRC = 0
NRCX = 0 NGRPX = 70 KFORM = 1
NTB = 0 BOXX = 0.000 BOXY = 0.000
BOXZ = 0.000 BETA = 0.000
NTF = 1 NTID = 0 NTN = 1
NTNB = 0 NSNB = 50 IDIEL = 0
RCUT = 12.00 SCNB = 2.00
SCEE = 1.20 DIELC = 1.00
IMAX EBMAX EANMAX EDIHMAX ENB14MAX
0 0.00 0.00 0.00 0.00
EEL14MAX ENBMAX EELMAX EHBMAX ECONSMAX
0.00 0.00 0.00 0.00 0.00
.....
++++++++++++++++++++++++++++++++++++++++++++++++++
Thanking you in advance
Prem
#############################################
Prem Raj B.J.
Dept. of Crystallography and Biophysics
University of Madras
Guindy Campus
Chennai 600 025
INDIA
email : prbj_at_hotmail.com
phone : 4353229 (residence) , 2351367 (Dept)
#############################################
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Received on Tue Jun 26 2001 - 09:34:38 PDT
