I don't have antechamebr in amber7 around, but I think you may solve this
problem by set -j flag to "none" (not judge atom type automatically) when
run antechamber
Best
Junmei
"Mi-Kyung Seo"
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com> To
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07/30/2003 02:00
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Dear Amber users,
Thanks for last reply.
I created new molecule in XLEaP(AMBER 7.0) and save it as prep file using
saveamberprep command.
This is Cartesian prep format.
I used antechamber to convert this cartesian prep(prepc) into internal
coordinates(prepi). Everything looks ok except atom type.
Converted internal coordinates prep doesn't seem to read correct atome type
and just show atom name twice.
Here are examples.:
This is Cartesian prep file :
--------------------------------------------------------------------------------------------
0 0 0
leap-generated prep residue
gal.res
gal INT 0
CHANGE NOMIT DU BEG
0.00000
1 DUMM DU M 0.000000 0.000000 0.000000 0.0
2 DUMM DU M 1.000000 0.000000 0.000000 0.0
3 DUMM DU M 1.000000 1.000000 0.000000 0.0
4 C1 CT M 0.000000 0.000000 0.000000 0.031400
5 C2 CT 3 1.500000 0.000000 0.000000 0.178700
6 H15 H1 E 1.833808 0.471322 0.816350 0.065100
7 C8 CT 3 2.000711 -1.413962 0.000002 0.255800
8 H20 H1 E 1.667853 -1.885954 -0.816349 0.096900
9 H21 H1 E 1.667853 -1.885952 0.816354 -0.022800
10 O9 OH S 3.500711 -1.413962 0.000004 -0.678700
11 H22 OH E 3.834519 -2.356603 0.000004 -0.678700
12 O3 OS E 2.000711 0.706980 -1.224527 -0.338300
13 O7 OH S -0.500711 -0.708491 1.223654 -0.630800
14 H19 HO E -0.167853 -1.651468 1.223071 0.438600
15 H14 H1 E -0.333808 -0.472327 -0.815769 0.067700
16 C6 CT M -0.500711 1.413962 0.000000 0.246500
17 O11 OH S -0.001424 2.121949 1.224527 -0.665300
18 H24 HO E -0.335233 3.064589 1.224528 0.418600
19 H18 H1 E -1.500711 1.413962 -0.000001 0.051500
20 C5 CT M -0.001424 2.121949 -1.224527 0.178700
21 O10 OH S -0.500711 1.415469 -2.449925 -0.659200
22 H23 OH E -1.500710 1.414968 -2.450798 -0.659200
23 H17 H1 E -0.335233 3.064589 -1.224528 0.124800
24 C4 AC M 1.501424 2.121445 -1.225399 0.129400
25 H16 H2 E 1.834282 2.593436 -0.409047 0.146800
26 O12 OG M 2.002137 2.828426 -2.449925 -0.411000
27 C13 CT M 3.502137 2.828426 -2.449923 0.059100
28 H25 H1 E 3.835944 3.299747 -1.633572 0.057300
29 H26 H1 E 3.835946 3.299748 -3.266273 0.057300
30 H27 H1 M 3.835945 1.885785 -2.449923 0.057300
------------------------------------------------------------------------------------------------
This is internal coordinates prep file:
----------------------------------------------------------------------------------------------
0 0 2
This is a remark line
molecule.res
gal XYZ 0
CORRECT OMIT DU BEG
0.0000
1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
4 O9 O9 M 3 2 1 1.540 111.208 180.000 -0.679
5 H22 H22 E 4 3 2 1.000 109.504 0.000 -0.679
6 C8 C8 M 4 3 2 1.500 0.000 -90.000 0.256
7 H20 H20 E 6 4 3 1.000 109.456 45.000 0.097
8 H21 H21 E 6 4 3 1.000 109.456 45.000 -0.023
9 C2 C2 M 6 4 3 1.500 109.510 45.000 0.179
10 H15 H15 E 9 6 4 1.000 109.423 -59.947 0.065
11 O3 O3 E 9 6 4 1.500 109.428 59.962 -0.338
12 C1 C1 M 9 6 4 1.500 109.510 -180.000 0.031
13 O7 O7 S 12 9 6 1.500 109.510 59.954 -0.631
14 H19 H19 E 13 12 9 1.000 109.451 -60.015 0.439
15 H14 H14 E 12 9 6 1.000 109.510 -59.954 0.068
16 C6 C6 M 12 9 6 1.500 109.510 180.000 0.246
17 O11 O11 S 16 12 9 1.501 109.477 -59.983 -0.665
18 H24 H24 E 17 16 12 1.000 109.481 179.994 0.419
19 H18 H18 E 16 12 9 1.000 109.510 -180.000 0.051
20 C5 C5 M 16 12 9 1.501 109.477 59.983 0.179
21 O10 O10 S 20 16 12 1.500 109.462 60.033 -0.659
22 H23 H23 E 21 20 16 1.000 109.519 60.047 -0.659
23 H17 H17 E 20 16 12 1.000 109.481 -179.994 0.125
24 C4 C4 M 20 16 12 1.502 109.444 -59.919 0.129
25 H16 H16 E 24 20 16 1.000 109.437 -60.096 0.147
26 O12 O12 M 24 20 16 1.500 109.486 179.965 -0.411
27 C13 C13 M 26 24 20 1.500 109.505 179.965 0.059
28 H25 H25 E 27 26 24 1.000 109.510 -60.038 0.057
29 H26 H26 E 27 26 24 1.000 109.510 -179.945 0.057
30 H27 H27 E 27 26 24 0.999 109.523 60.009 0.057
---------------------------------------------------------------------------------------
I saved new molecule as prep because I need internal coordinates prep file.
Thanks.
Mikyung
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Received on Wed Jul 30 2003 - 20:53:01 PDT
