Nevermind, I had to source /software/amber/amber9.sh beforehand.
--- On Wed, 1/25/12, rainy908 <rainy908.yahoo.com> wrote:
> From: rainy908 <rainy908.yahoo.com>
> Subject: [AMBER] divcon: error while loading shared libraries: libvml.so: cannot open shared object file
> To: amber.ambermd.org
> Date: Wednesday, January 25, 2012, 11:21 AM
> 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 - 11:30:04 PST
