AMBER Archive (2002)

Subject: This one with anal in amber6

From: Prabal Maiti (maiti_at_wag.caltech.edu)
Date: Fri Jul 12 2002 - 13:09:39 CDT

I did the analysis for the same 10-mer DNA as in my previous email with
anal in AMBER6.

Here also I see that the group energy are different at the begining and at
the end (in the order they are printed in anal output).

ENERGY CONTRIBUTION BY GROUPS
1 -149.472000
2 -196.461000
3 -120.201000
4 -169.040000
5 -159.504000
6 -191.575000
7 -168.044000
8 -64.154000
9 -125.126000
10 -114.397000
11 -132.681000
12 -166.969000
13 -67.345000
14 -139.577000
15 -148.896000
16 -151.668000
17 -157.445000
18 -49.034000
19 -119.173000
20 -110.527000
21 -16819.504000

INDIVIDUAL GROUPS INTERACTION

1 -176.330000
2 -274.440000
3 -196.800000
4 -252.220000
5 -237.910000
6 -255.210000
7 -217.450000
8 -117.980000
9 -170.870000
10 -146.200000
11 -146.080000
12 -210.150000
13 -93.820000
14 -200.570000
15 -218.440000
16 -173.840000
17 -190.140000
18 -95.250000
19 -165.000000
20 -145.290000
21 -20043.610000

Now which group energy is correct. In AMBER web page it is said that this
things have been fixed in AMBER7. But I see same problem. I want to modify
SANDER code itself to give me output per atom in a user defined
interval. From there group energy can be exttracted by adding the
energy of atoms belonging to same group. Can someone help me in this (like
pointing out exactly which routines to look for for non-bond interaction
etc). It is difficult because my knowledge of fortarn is very poor. Or Any
amber developer can probably help me in this. It should be quite
straingforward for them. I have implemented this in my own code in the
following way: For non-bond VDW I divide the energy 1/2:12 ration in two
atoms. For bond stretching also 1/2:12 ratio. For angle I put the energy
on the middle atom, and for torsion in 1/2:1/2 ration for the middle two
atoms. For PME/EWALD I get the effective field acting on each atom and and
multiplied by charge give me the energy for that atom. Sum of all the
energy ofcourse gives the total energy/ If same thing can be done in
sander that will be great.

Thanks
Prabal 

-- 
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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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