Hi,
I'm encountering the following error involving divcon when executing antechamber. I have no idea how to go about solving it. Can someone please help? thanks.
$AMBERHOME/exe/antechamber -i frame0_desmond_3-out_gtp_h.ac -fi ac -o frame0_desmond_3-out_gtp_h.prepin -fo prepi -c bcc
Total number of electrons: 266; net charge: 0
Running: $AMBERHOME/exe/divcon
/software/amber/amber9/exe/divcon: error while loading shared libraries: libvml.so: cannot open shared object file: No such file or directory
Error: cannot run "$AMBERHOME/exe/divcon" of bcc() in charge.c properly, exit
My input *.ac file is provided below:
CHARGE 0.00 ( 0 )
Formula: H14 C10 N5 O14 P3
ATOM 1 PA GTP 1 -7.349 0.737 -0.920 0.000000 p5
ATOM 2 O1A GTP 1 -8.784 1.425 -1.173 0.000000 o
ATOM 3 O2A GTP 1 -7.073 -0.461 -1.763 0.000000 o
ATOM 4 O5' GTP 1 -6.356 1.997 -1.121 0.000000 os
ATOM 5 O3A GTP 1 -7.298 0.439 0.662 0.000000 os
ATOM 6 PB GTP 1 -6.212 -0.588 1.301 0.000000 p5
ATOM 7 O2B GTP 1 -4.831 -0.051 1.530 0.000000 oh
ATOM 8 C5' GTP 1 -5.046 1.785 -1.602 0.000000 c3
ATOM 9 C4' GTP 1 -5.056 1.546 -3.127 0.000000 c3
ATOM 10 O1B GTP 1 -6.238 -1.789 0.201 0.000000 o
ATOM 11 O3B GTP 1 -6.994 -1.268 2.572 0.000000 os
ATOM 12 PG GTP 1 -7.371 -0.732 4.064 0.000000 p5
ATOM 13 O2G GTP 1 -8.563 -1.722 4.509 0.000000 o
ATOM 14 O3G GTP 1 -6.322 -0.659 5.115 0.000000 oh
ATOM 15 O4' GTP 1 -5.936 2.519 -3.695 0.000000 os
ATOM 16 C3' GTP 1 -3.677 1.828 -3.752 0.000000 c3
ATOM 17 O3' GTP 1 -3.433 1.150 -4.973 0.000000 oh
ATOM 18 C2' GTP 1 -3.747 3.310 -4.080 0.000000 c3
ATOM 19 O1G GTP 1 -8.233 0.599 3.826 0.000000 o
ATOM 20 O2' GTP 1 -2.918 3.643 -5.193 0.000000 oh
ATOM 21 C1' GTP 1 -5.238 3.492 -4.385 0.000000 c3
ATOM 22 N9 GTP 1 -5.672 4.827 -3.902 0.000000 na
ATOM 23 C4 GTP 1 -5.335 6.028 -4.479 0.000000 cc
ATOM 24 C5 GTP 1 -5.953 7.012 -3.736 0.000000 cd
ATOM 25 C6 GTP 1 -5.779 8.387 -4.124 0.000000 c
ATOM 26 N7 GTP 1 -6.668 6.433 -2.691 0.000000 nd
ATOM 27 N1 GTP 1 -4.976 8.522 -5.258 0.000000 n
ATOM 28 O6 GTP 1 -6.224 9.415 -3.617 0.000000 o
ATOM 29 C8 GTP 1 -6.480 5.146 -2.834 0.000000 cc
ATOM 30 C2 GTP 1 -4.398 7.460 -5.938 0.000000 cd
ATOM 31 N2 GTP 1 -3.660 7.718 -7.019 0.000000 nh
ATOM 32 N3 GTP 1 -4.535 6.200 -5.580 0.000000 nc
ATOM 33 H5'1GTP 1 -4.465 2.666 -1.337 0.000000 h1
ATOM 34 H5'2GTP 1 -4.592 0.936 -1.088 0.000000 h1
ATOM 35 H4' GTP 1 -5.402 0.539 -3.362 0.000000 h1
ATOM 36 H3' GTP 1 -2.861 1.599 -3.066 0.000000 h1
ATOM 37 HO3 GTP 1 -2.980 1.810 -5.492 0.000000 ho
ATOM 38 H2' GTP 1 -3.483 3.899 -3.200 0.000000 h1
ATOM 39 HO2 GTP 1 -3.190 4.523 -5.439 0.000000 ho
ATOM 40 H1' GTP 1 -5.498 3.452 -5.444 0.000000 h2
ATOM 41 HN1 GTP 1 -4.862 9.480 -5.538 0.000000 hn
ATOM 42 HN2 GTP 1 -3.277 6.929 -7.520 0.000000 hn
ATOM 43 H9 GTP 1 -3.513 8.651 -7.366 0.000000 hn
ATOM 44 H8 GTP 1 -6.918 4.396 -2.177 0.000000 h5
ATOM 45 H7 GTP 1 -4.278 -0.739 1.908 0.000000 ho
ATOM 46 H6 GTP 1 -6.706 -0.325 5.929 0.000000 ho
BOND 1 1 2 9 PA O1A
BOND 2 1 3 9 PA O2A
BOND 3 1 4 1 PA O5'
BOND 4 1 5 1 PA O3A
BOND 5 4 8 1 O5' C5'
BOND 6 5 6 1 O3A PB
BOND 7 6 7 1 PB O2B
BOND 8 6 10 2 PB O1B
BOND 9 6 11 1 PB O3B
BOND 10 7 45 1 O2B H7
BOND 11 8 9 1 C5' C4'
BOND 12 8 33 1 C5' H5'1
BOND 13 8 34 1 C5' H5'2
BOND 14 9 15 1 C4' O4'
BOND 15 9 16 1 C4' C3'
BOND 16 9 35 1 C4' H4'
BOND 17 11 12 1 O3B PG
BOND 18 12 13 9 PG O2G
BOND 19 12 14 1 PG O3G
BOND 20 12 19 9 PG O1G
BOND 21 14 46 1 O3G H6
BOND 22 15 21 1 O4' C1'
BOND 23 16 17 1 C3' O3'
BOND 24 16 18 1 C3' C2'
BOND 25 16 36 1 C3' H3'
BOND 26 17 37 1 O3' HO3
BOND 27 18 20 1 C2' O2'
BOND 28 18 21 1 C2' C1'
BOND 29 18 38 1 C2' H2'
BOND 30 20 39 1 O2' HO2
BOND 31 21 22 1 C1' N9
BOND 32 21 40 1 C1' H1'
BOND 33 22 23 7 N9 C4
BOND 34 22 29 7 N9 C8
BOND 35 23 24 8 C4 C5
BOND 36 23 32 1 C4 N3
BOND 37 24 25 1 C5 C6
BOND 38 24 26 7 C5 N7
BOND 39 25 27 1 C6 N1
BOND 40 25 28 2 C6 O6
BOND 41 26 29 8 N7 C8
BOND 42 27 30 1 N1 C2
BOND 43 27 41 1 N1 HN1
BOND 44 29 44 1 C8 H8
BOND 45 30 31 1 C2 N2
BOND 46 30 32 2 C2 N3
BOND 47 31 42 1 N2 HN2
BOND 48 31 43 1 N2 H9
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Received on Wed Jan 25 2012 - 11:30:03 PST
