Can someone give me some advice on this.
Prabal
---------- Forwarded message ----------
Date: Fri, 5 Jul 2002 16:00:55 -0700 (PDT)
From: Prabal Maiti <maiti_at_intel4.wag.caltech.edu>
To: AMBER mailing list <amber_at_heimdal.compchem.ucsf.edu>
Subject: anal in AMBER7 gives inconsistent results with itself
I was trying to get the energy for each of the residue in a 10-mer B-DNA.
I used 20A cutoff.
>From the initial energy components Total energy : -19163.2768
>From the ENERGY CONTRIBUTION BY GROUPS Tot. Ener: -19288.405
>From the INDIVIDUAL GROUPS INTERACTION Tot. Ener: -57489.83
Here are the relevent part of the results using anal in AMBER7:
INITIAL ENERGY COMPONENTS
TOTAL ENERGY = -19163.2768
NON-BONDED VDW ENERGY = 2094.5210
NON-BONDED EEL ENERGY = -19166.4269
HBOND 10-12 ENERGY = 0.0000
BOND ENERGY = 180.7166
ANGLE ENERGY = 334.6828
DIHEDRAL ENERGY = 358.8721
NON-BOND 14 VDW ENERGY = 174.3331
NON-BOND 14 EEL ENERGY = -3139.9756
BOND CONSTRAINT ENERGY = 0.0000
ANGLE CONSTRAINT ENERGY = 0.0000
DIHEDRAL CONSTRAINT ENERGY = 0.0000
POSITION CONSTRAINT ENERGY = 0.0000
ENERGY CONTRIBUTION BY GROUPS (seperate contributioin from
non-bond/bonded interaction are not shown)
GROUP TOTAL
1 -165.426000
2 -204.285000
3 -78.226000
4 -144.510000
5 -152.719000
6 -142.428000
7 -158.099000
8 -28.267000
9 -109.113000
10 -106.932000
11 -139.703000
12 -166.251000
13 -94.740000
14 -130.970000
15 -110.424000
16 -153.368000
17 -142.025000
18 0.788000
19 -83.728000
20 -85.661000
21 -16767.18900
TOTAL -19288.405
INDIVIDUAL GROUPS INTERACTION
GROUP INTRA INTER TOTAL
1 54.26 -18735.35 -18681.09
2 234.40 -2964.92 -2730.52
3 2058.58 -3050.21 -991.63
4 -19240.39 -19301.23 -38541.61
5 -82.03 -141.37 -223.40
6 -116.61 -51.64 -168.25
7 -121.46 -73.28 -194.74
8 -12.67 -31.20 -43.86
9 -81.26 -55.70 -136.97
10 -83.23 -47.40 -130.63
11 -124.04 -31.32 -155.36
12 -121.40 -89.71 -211.11
13 -35.81 -117.87 -153.67
14 -67.97 -126.01 -193.97
15 -72.37 -76.11 -148.48
16 -125.18 -56.37 -181.55
17 -125.58 -32.89 -158.47
18 -6.42 14.42 8.00
19 -77.71 -12.05 -89.75
20 -82.11 -7.10 -89.21
21 -14828.73 -3876.92 -18705.65
TOTAL -33057.72 -24432.11 -57489.83
Any suggestion whats going wrong. I did correct the bugfix.12 as given in
AMBER web page. Is there any way I can output the energy per atom (with
proper break up for valence parts) during sander runs. Did anyone modify
the code to give this output.
Thanks
Prabal
--
------------------------------------------------------------------------
Prabal K Maiti Email:maiti_at_wag.caltech.edu
Beckman Institute (139-74) pkmaiti_at_yahoo.com
California Institute of Technology Tel:626-395-8151 (O)
400 South Wilson Avenue :626-744-1363 (H)
Pasadena, CA 91125 Fax:626-585-0918
Home add: 110 S. Michigan Ave.
http://www.wag.caltech.edu/home/maiti Apt # 19, Pasadena, CA 91106
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Received on Fri Jul 12 2002 - 10:38:19 PDT
