Dear Amber users,
I am using Amber 9.0 for simulation. I am try to use 'ANAL' module
for calculating the interaction energy matrix. But something wrong happens
with the output files. Even though Anal reads the input groups correctly
but it is not write the energy for all the groups in the output file (
energy values are showing zero) as shown below
*Input group read correctly......
*
***************************************************************************************************************************
NUMBER OF ATOMS = 1222
loading the groups for analysis
----- READING GROUP 1; TITLE:
MOL_1
GRP 1 RES 35 TO 58
Number of atoms in this group = 758
----- READING GROUP 2; TITLE:
MOL_2
cation
ALL ATOMS THAT MEET 1 OF THE FOLLOWING SPECIFICATIONS WILL BE INCLUDED
IN GROUP BELOW
GRAPH NAME = H1 SYMBOL = * TREE SYMBOL = * RESIDUE TYPE
= *
GRP 2 RES 1 TO 12
GRP 2 RES 14 TO 22
GRP 2 RES 24 TO 34
Number of atoms in this group = 15
----- READING GROUP 3; TITLE:
MOL_3
GRP 3 RES 1 TO 12
GRP 3 RES 14 TO 22
GRP 3 RES 24 TO 34
Number of atoms in this group = 392
----- END OF GROUP READ -----
non-bonded pairs are generated in residue base
and stored as residue pairs
number of non-bonded residue pairs = 3240
individual pair energies greater than 10.00 kcal/mol:
*************************************************************************************************************************
*no energy for Group TWO..................*
*************************************************************************************************************************
TOTAL INTERACTION ENERGY MATRIX
1 2 3 4
1 1353.628 0.000 -353.658 -6353.627
2 0.000 0.000 0.000 0.000
3 -353.658 0.000 49.594 -440.323
4 -6353.627 0.000 -440.323 2675.458
INDIVIDUAL GROUPS INTERACTION
GROUP INTRA INTER TOTAL
1 1353.63 -6707.28 -5353.66
2 0.00 0.00 0.00
3 49.59 -793.98 -744.39
4 2675.46 -6793.95 -4118.49
*****************************************************************************************************************************
*
When I tried by changing the group, Anal showing some weird results in the
output file as shown below.........*
*****************************************************************************************************************************
NUMBER OF ATOMS = 1222
loading the groups for analysis
----- READING GROUP 1; TITLE:
MOL_1
GRP 1 RES 35 TO 58
Number of atoms in this group = 758
----- READING GROUP 2; TITLE:
*MOL_2
GRP 2 RES 1 TO 12
GRP 2 RES 14 TO 22
GRP 2 RES 24 TO 34
Number of atoms in this group = 392
----- READING GROUP 3; TITLE:
MOL_3
GRP 3 RES 1 TO 12
GRP 3 RES 14 TO 22
GRP 3 RES 24 TO 34
Number of atoms in this group = 392*
----- END OF GROUP READ -----
non-bonded pairs are generated in residue base
and stored as residue pairs
number of non-bonded residue pairs = 3240
individual pair energies greater than 10.00 kcal/mol:
*************************************************************************************************************************
*Even though the group 2 and 3 ( MOL_2 & MOL_3) are same, there is no energy
values written for Group 2 in the output*.
*******************************************************************************************************************************
TOTAL INTERACTION ENERGY MATRIX
1 2 3 4
1 1355.437 0.000 -485.420 -6381.657
2 0.000 0.000 0.000 0.000
3 -485.420 0.000 98.573 -403.917
4 -6381.657 0.000 -403.917 2677.581
INDIVIDUAL GROUPS INTERACTION
GROUP INTRA INTER TOTAL
1 1355.44 -6867.08 -5511.64
2 0.00 0.00 0.00
3 98.57 -889.34 -790.76
4 2677.58 -6785.57 -4107.99
************************************************************************************************************************************
*In the Anal output I can also able to see some error mesages
like................ *
*********************************************************************************************************************
1- 1 1104- 1111 (P -CT) 1-4 Interaction 4.07 -0.073
12.903
*DIHEDRAL ANGLE ERROR (??): 1513 3495 3498 3507 3510
DIHEDRAL ANGLE ERROR (??): 1514 3495 3498 3507 3510
DIHEDRAL ANGLE ERROR (??): 1515 3495 3498 3507 351*0
1- 1 1155- 1159 (N2-C ) 1-4 Interaction 3.51 -0.049
-61.261
1- 1 1154- 1160 (CA-O ) 1-4 Interaction 3.37 -0.056
-45.356
1- 1 1152- 1159 (CM-C ) 1-4 Interaction 2.77 1.388
-41.451
1- 1 1146- 1166 (OS-OS) 1-4 Interaction 3.51 -0.081
15.203
1- 1 1146- 1159 (OS-C ) 1-4 Interaction 3.60 -0.060
-22.552
1- 1 1144- 1167 (CT-P ) 1-4 Interaction 3.99 -0.074
13.182
1- 1 1140- 1146 (OS-OS) 1-4 Interaction 3.12 -0.055
16.240
* DIHEDRAL ANGLE ERROR (??): 1560 3417 3420 3429 3480
DIHEDRAL ANGLE ERROR (??): 1561 3417 3420 3429 3480
DIHEDRAL ANGLE ERROR (??): 1562 3417 3420 3429 3480*
1- 1 1137- 1144 (P -CT) 1-4 Interaction 4.05 -0.074
12.980
***********************************************************************************************************************
Can anyone help me to figure out this problem?
Thanks in advance
Sincerely
Aneesh
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Received on Tue Dec 21 2010 - 01:00:02 PST
