I tried to post this a few weeks ago but it seems it never made it to
the mailing list. My apologies if this is a repeat.
I've been trying to create a prmtop file for a sphingolipid, however
xleap (Amber9 and AmberTools versions) crashes and issues a
"Segmentation fault" when I issue the SaveAmberParm command. The
AmberTools version of xleap gives a bit more information on crashing.
Here's the output I get:
> /opt/amber10/bin/xleap -s -f glccer.leaprc
-I: Adding /opt/amber10/dat/leap/prep to search path.
-I: Adding /opt/amber10/dat/leap/lib to search path.
-I: Adding /opt/amber10/dat/leap/parm to search path.
-I: Adding /opt/amber10/dat/leap/cmd to search path.
-s: Ignoring startup file: leaprc
-f: Source glccer.leaprc.
/opt/amber10/bin/xleap: line 9: 13401 Segmentation
Fault /opt/amber10/bin/xaLeap -I/opt/amber10/dat/leap/prep -
I/opt/amber10/dat/leap/lib -I/opt/amber10/dat/leap/parm -
I/opt/amber10/dat/leap/cmd $*
The number between "line 9" and "Segmentation fault" changes with each
crash. The file "glccer.leaprc" is as follows:
source leaprc.gaff
# load residues
LoadAmberPrep stearate.prepin
LoadAmberPrep sphingosine.prepin
LoadAmberPrep glucose.prepin
# set connection atoms to link residues
set STE.1 connect1 STE.1.C1
set STE tail STE.1.C1
set SPH.1 connect0 SPH.1.N2
set SPH.1 connect1 SPH.1.O1
set SPH head SPH.1.N2
set SPH tail SPH.1.O1
# combine residues into one new molecule
GLCCER = sequence { STE SPH GLC }
# correct incorect Glucose linkage
deletebond GLCCER.2.O1 GLCCER.3.O4
bond GLCCER.2.O1 GLCCER.3.C1
# remove atoms eliminated in linkages
remove GLCCER GLCCER.STE.O1'
remove GLCCER GLCCER.STE.HO1
remove GLCCER GLCCER.SPH.HN23
remove GLCCER GLCCER.SPH.HO1
remove GLCCER GLCCER.GLC.H11
# make double bond b/w SPH C8 and C9
remove GLCCER GLCCER.SPH.H83
remove GLCCER GLCCER.SPH.H93
# make hydroxyl at STE C2
set GLCCER.STE.H23 name O2
set GLCCER.STE.O2 element O
set GLCCER.STE.O2 type oh
set GLCCER.STE.O2 charge -0.62703
h1 = CreateAtom HO2 ho 0.417
set h1 element H
add GLCCER h1
bond GLCCER.STE.O2 h1
# save prmtop and inpcrd files
SaveAmberParm GLCCER glccer.prmtop glccer.inpcrd
The prep files stearate.prepin, sphingosine.prepin and glucose.prepin
were prepared using GAFF and are attached.
Can anyone tell me what I'm doing wrong?
Brendan
--
Brendan Duggan <bmduggan.musc.edu>
Medical University of South Carolina
0 0 2
This is a remark line
molecule.res
STE INT 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 O1 o M 3 2 1 1.540 111.208 180.000 -0.55500
5 C1 c M 4 3 2 1.209 161.582 94.054 0.63403
6 O1' oh S 5 4 3 1.308 120.864 -87.339 -0.60719
7 HO1 ho E 6 5 4 0.972 106.599 -87.072 0.44353
8 C2 c3 M 5 4 3 1.520 121.024 68.118 -0.12516
9 H23 hc E 8 5 4 1.093 107.844 84.777 0.08012
10 H22 hc E 8 5 4 1.093 108.276 -30.740 0.08063
11 C3 c3 M 8 5 4 1.547 115.491 -152.962 -0.07768
12 H33 hc E 11 8 5 1.093 109.699 67.655 0.05153
13 H32 hc E 11 8 5 1.094 110.854 -51.447 0.06270
14 C4 c3 M 11 8 5 1.534 109.505 -171.220 -0.08011
15 H43 hc E 14 11 8 1.093 109.217 61.876 0.04084
16 H42 hc E 14 11 8 1.093 109.622 -55.879 0.04096
17 C5 c3 M 14 11 8 1.536 111.761 -177.327 -0.07844
18 H53 hc E 17 14 11 1.093 110.095 60.314 0.04212
19 H52 hc E 17 14 11 1.094 110.207 -58.552 0.04279
20 C6 c3 M 17 14 11 1.535 108.751 -179.103 -0.07933
21 H63 hc E 20 17 14 1.094 109.580 59.350 0.03990
22 H62 hc E 20 17 14 1.093 109.609 -58.543 0.03997
23 C7 c3 M 20 17 14 1.532 110.999 -179.631 -0.07881
24 H73 hc E 23 20 17 1.093 109.780 59.107 0.04036
25 H72 hc E 23 20 17 1.093 109.868 -59.357 0.04043
26 C8 c3 M 23 20 17 1.535 109.727 179.869 -0.07921
27 H83 hc E 26 23 20 1.093 109.874 59.241 0.03956
28 H82 hc E 26 23 20 1.094 109.844 -59.084 0.03961
29 C9 c3 M 26 23 20 1.533 109.934 -179.829 -0.07877
30 H93 hc E 29 26 23 1.093 109.739 59.030 0.03990
31 H92 hc E 29 26 23 1.093 109.661 -59.183 0.03991
32 C10 c3 M 29 26 23 1.533 110.188 179.956 -0.07921
33 H10 hc E 32 29 26 1.094 109.820 59.151 0.03945
34 H19 hc E 32 29 26 1.094 109.788 -59.217 0.03947
35 C11 c3 M 32 29 26 1.534 109.816 179.978 -0.07874
36 H11 hc E 35 32 29 1.094 109.671 59.112 0.03972
37 H20 hc E 35 32 29 1.093 109.685 -59.124 0.03972
38 C12 c3 M 35 32 29 1.533 110.104 179.948 -0.07918
39 H12 hc E 38 35 32 1.094 109.645 59.161 0.03940
40 H21 hc E 38 35 32 1.093 109.717 -59.091 0.03941
41 C13 c3 M 38 35 32 1.535 110.035 179.963 -0.07878
42 H13 hc E 41 38 35 1.093 109.651 59.134 0.03962
43 H24 hc E 41 38 35 1.093 109.671 -59.028 0.03961
44 C14 c3 M 41 38 35 1.535 110.155 -179.978 -0.07911
45 H14 hc E 44 41 38 1.094 109.587 59.100 0.03939
46 H25 hc E 44 41 38 1.093 109.598 -58.966 0.03941
47 C15 c3 M 44 41 38 1.537 110.342 -179.944 -0.07894
48 H15 hc E 47 44 41 1.093 109.574 58.956 0.03941
49 H26 hc E 47 44 41 1.094 109.522 -58.979 0.03940
50 C16 c3 M 47 44 41 1.537 110.359 -179.957 -0.07936
51 H16 hc E 50 47 44 1.093 109.500 58.880 0.03935
52 H27 hc E 50 47 44 1.093 109.437 -58.929 0.03936
53 C17 c3 M 50 47 44 1.539 110.741 180.000 -0.08010
54 H17 hc E 53 50 47 1.094 109.740 59.028 0.03838
55 H28 hc E 53 50 47 1.093 109.757 -59.069 0.03838
56 C18 c3 M 53 50 47 1.538 110.678 179.941 -0.09258
57 H18 hc E 56 53 50 1.092 110.293 179.985 0.03239
58 H29 hc E 56 53 50 1.093 110.498 60.111 0.03245
59 H30 hc E 56 53 50 1.093 110.544 -60.092 0.03247
LOOP
IMPROPER
C2 O1 C1 O1'
DONE
STOP
0 0 2
This is a remark line
molecule.res
SPH INT 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 O1 oh M 3 2 1 1.540 111.208 180.000 -0.60427
5 HO1 ho E 4 3 2 0.960 146.453 -39.723 0.40400
6 C1 c3 M 4 3 2 1.430 37.396 -28.247 0.12528
7 H13 h1 E 6 4 3 1.089 109.446 -80.575 0.03390
8 H12 h1 E 6 4 3 1.088 109.435 159.510 0.02476
9 C2 c3 M 6 4 3 1.527 109.509 39.458 0.14403
10 N2 n3 B 9 6 4 1.496 109.483 -60.018 -0.91489
11 HN22 hn E 10 9 6 1.035 109.453 59.999 0.36693
12 HN23 hn E 10 9 6 1.010 109.444 179.962 0.35592
13 H23 h1 E 9 6 4 1.088 109.501 59.944 0.04374
14 C3 c3 M 9 6 4 1.528 109.489 -179.969 0.17611
15 O3 oh S 14 9 6 1.431 109.463 -60.025 -0.59658
16 HO3 ho E 15 14 9 0.970 109.940 59.958 0.39880
17 H33 h1 E 14 9 6 1.088 109.481 59.987 0.05040
18 C4 c2 M 14 9 6 1.511 109.473 -179.976 -0.17939
19 H43 ha E 18 14 9 1.079 120.006 59.938 0.14049
20 C5 c2 M 18 14 9 1.340 119.956 -120.027 -0.15788
21 H53 ha E 20 18 14 1.080 120.022 -0.051 0.13194
22 C6 c3 M 20 18 14 1.510 119.981 -179.989 -0.05084
23 H62 hc E 22 20 18 1.088 109.463 -60.043 0.04774
24 H63 hc E 22 20 18 1.088 109.500 60.010 0.04835
25 C7 c3 M 22 20 18 1.529 109.474 179.978 -0.07674
26 H72 hc E 25 22 20 1.088 109.490 -59.987 0.04458
27 H73 hc E 25 22 20 1.089 109.434 60.010 0.04136
28 C8 c3 M 25 22 20 1.528 109.467 179.946 -0.07977
29 H82 hc E 28 25 22 1.088 109.519 -59.951 0.03918
30 H83 hc E 28 25 22 1.089 109.439 60.067 0.04051
31 C9 c3 M 28 25 22 1.529 109.467 180.000 -0.07885
32 H92 hc E 31 28 25 1.088 109.457 -59.963 0.04043
33 H93 hc E 31 28 25 1.088 109.429 60.043 0.03993
34 C10 c3 M 31 28 25 1.528 109.452 -179.964 -0.07912
35 H102 hc E 34 31 28 1.088 109.497 -59.974 0.03943
36 H103 hc E 34 31 28 1.090 109.490 60.020 0.03973
37 C11 c3 M 34 31 28 1.529 109.452 -180.000 -0.07891
38 H112 hc E 37 34 31 1.088 109.457 -59.999 0.03976
39 H113 hc E 37 34 31 1.088 109.429 60.007 0.03961
40 C12 c3 M 37 34 31 1.528 109.452 180.000 -0.07908
41 H122 hc E 40 37 34 1.097 108.513 -59.571 0.03942
42 H123 hc E 40 37 34 1.090 109.490 60.020 0.03956
43 C13 c3 M 40 37 34 1.529 109.452 -180.000 -0.07889
44 H132 hc E 43 40 37 1.088 109.490 -59.969 0.03958
45 H133 hc E 43 40 37 1.088 109.429 60.007 0.03951
46 C14 c3 M 43 40 37 1.528 109.475 -179.987 -0.07903
47 H142 hc E 46 43 40 1.089 109.421 -59.996 0.03941
48 H143 hc E 46 43 40 1.089 109.310 59.810 0.03946
49 C15 c3 M 46 43 40 1.528 109.458 -179.987 -0.07898
50 H152 hc E 49 46 43 1.088 109.488 -59.993 0.03937
51 H153 hc E 49 46 43 1.089 109.453 60.014 0.03935
52 C16 c3 M 49 46 43 1.528 109.473 179.964 -0.07935
53 H162 hc E 52 49 46 1.088 109.451 -59.941 0.03936
54 H163 hc E 52 49 46 1.089 109.402 60.001 0.03939
55 C17 c3 M 52 49 46 1.527 109.477 179.964 -0.08008
56 H172 hc E 55 52 49 1.088 109.516 -59.938 0.03836
57 H173 hc E 55 52 49 1.089 109.422 60.067 0.03836
58 C18 c3 M 55 52 49 1.526 109.479 179.995 -0.09256
59 H181 hc E 58 55 52 1.088 109.518 -179.964 0.03229
60 H183 hc E 58 55 52 1.090 109.446 60.045 0.03245
61 H182 hc E 58 55 52 1.091 109.282 -59.882 0.03243
LOOP
IMPROPER
C5 C3 C4 H43
C4 C6 C5 H53
DONE
STOP
0 0 2
This is a remark line
molecule.res
GLC INT 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 O4 oh M 3 2 1 1.540 111.208 180.000 -0.60225
5 HO4 ho E 4 3 2 0.976 17.354 87.639 0.42644
6 C4 c3 M 4 3 2 1.438 107.438 179.165 0.12075
7 H4 h1 E 6 4 3 1.096 109.108 -53.872 0.06355
8 C3 c3 M 6 4 3 1.541 110.616 65.907 0.07220
9 H3 h1 E 8 6 4 1.096 109.375 53.256 0.04873
10 O3 oh S 8 6 4 1.435 110.023 -66.986 -0.60620
11 HO3 ho E 10 8 6 0.978 107.199 -176.130 0.42392
12 C2 c3 M 8 6 4 1.555 110.801 173.140 0.06992
13 H2 h1 E 12 8 6 1.096 108.909 66.578 0.10314
14 O2 oh S 12 8 6 1.431 109.495 -173.337 -0.58982
15 HO2 ho E 14 12 8 0.978 109.062 60.195 0.40220
16 C1 c3 M 12 8 6 1.546 110.582 -52.042 0.09978
17 H1 h1 E 16 12 8 1.096 109.931 173.596 0.08705
18 H11 h1 E 16 12 8 1.095 110.475 -65.989 0.03314
19 O5 os M 16 12 8 1.444 109.498 54.119 -0.39649
20 C5 c3 M 19 16 12 1.457 115.702 -60.807 0.09989
21 H5 h1 E 20 19 16 1.094 108.748 -58.323 0.06043
22 C6 c3 M 20 19 16 1.541 109.548 -178.684 0.13717
23 H61 h1 E 22 20 19 1.096 108.846 -58.583 0.08874
24 H62 h1 E 22 20 19 1.095 109.550 -176.681 0.04716
25 O6 oh M 22 20 19 1.435 112.051 62.562 -0.59107
26 HO6 ho E 25 22 20 0.974 108.733 77.894 0.40163
LOOP
C5 C4
IMPROPER
DONE
STOP
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Received on Fri Apr 18 2008 - 21:19:37 PDT
