Your AmberTool11 with Amber10 went well because it invoked mopac.sh to
calculate the charge, and mopac didn't give error with your ligand. Your
AmberTool13 with Amber12 failed with the same ligand because it invoked sqm
program to calculate the charge, and sqm had problem with your ligand. You
need to look into the output file of sqm, i.e. sqm.out in your case, to
find out what is the problem with sqm.
Hope this helps!
Junjun
On Tue, May 13, 2014 at 2:44 PM, Biao Ma <jackyma1981.gmail.com> wrote:
> Hi, amber users.
>
> when I perform antechamber (Amber12, AmberTools13), I got the follow
> errors.
>
>
> Error: cannot run "/usr/local/amber12/bin/sqm -O -i sqm.in -o sqm.out" of
> > bcc() in charge.c properly, exit
>
>
> However, I can perform it successful at Amber10, AmberTools11 environment
> use the same files.
>
>
> I also try to redo the tutorial:
> http://ambermd.org/tutorials/basic/tutorial4b/ , but I got the same Error
> about "spm."
>
>
> Can anyone give me some hint?
>
>
> Thanks a lot.
>
> $ ./antechamber.sh cmd002
>
> Running: /usr/local/amber12/bin/bondtype -j full -i
> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
>
> Running: /usr/local/amber12/bin/atomtype -i ANTECHAMBER_AC.AC0 -o
> ANTECHAMBER_AC.AC -p gaff
>
> Total number of electrons: 246; net charge: 0
>
> Running: /usr/local/amber12/bin/sqm -O -i sqm.in -o sqm.out
>
> forrtl: severe (168): Program Exception - illegal instruction
>
> Image PC Routine Line Source
>
> sqm 0000000000451D2B Unknown Unknown Unknown
>
> sqm 000000000040AB89 Unknown Unknown Unknown
>
> sqm 0000000000401D8C Unknown Unknown Unknown
>
> libc.so.6 00000037FBE1D9C4 Unknown Unknown Unknown
>
> sqm 0000000000401C99 Unknown Unknown Unknown
>
> Error: cannot run "/usr/local/amber12/bin/sqm -O -i sqm.in -o sqm.out" of
> bcc() in charge.c properly, exit
>
> ### the stdio of at amber10 environment:
>
> $ ./antechamber.sh cmd002
>
> Running: /home/ma/amber10/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0
> -o ANTECHAMBER_BOND_TYPE.AC -f ac
>
> Running: /home/ma/amber10/bin/atomtype -i ANTECHAMBER_AC.AC0 -o
> ANTECHAMBER_AC.AC -p gaff
>
> Total number of electrons: 246; net charge: 0
>
> Running: /home/ma/amber10/bin/mopac.sh
>
> Running: /home/ma/amber10/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o
> ANTECHAMBER_AM1BCC.AC -f ac -p
> /home/ma/amber10/dat/antechamber/BCCPARM.DAT
> -s 2 -j 1
>
> Running: /home/ma/amber10/bin/atomtype -f ac -p bcc -o
> ANTECHAMBER_AM1BCC.AC-i
> ANTECHAMBER_AM1BCC_PRE.AC
>
> Running: /home/ma/amber10/bin/atomtype -i ANTECHAMBER_PREP.AC0 -o
> ANTECHAMBER_PREP.AC -p gaff
>
> Running: /home/ma/amber10/bin/prepgen -i ANTECHAMBER_PREP.AC -f int -o
> cmd002.prepin -rn "RES" -rf molecule.res
>
>
>
> my script is
>
> #!/bin/sh
>
> inp=$1
>
> antechamber -i $inp.pdb -fi pdb -o $inp.prepin -fo prepi -c bcc -s 2
>
> my Ligand is cmd002.pdb
>
> HETATM 1665 H01 RES 1 10.949 8.058 5.652 1.00 20.00
> H
>
> HETATM 1666 N1 RES 1 4.648 6.316 7.326 1.00 20.00
> N
>
> HETATM 1667 S1 RES 1 5.435 6.888 8.763 1.00 20.00
> S
>
> HETATM 1668 O1 RES 1 5.512 5.803 9.723 1.00 20.00
> O
>
> HETATM 1669 C1 RES 1 12.297 7.831 7.162 1.00 20.00
> C
>
> HETATM 1670 C10 RES 1 7.343 7.258 6.805 1.00 20.00
> C
>
> HETATM 1671 1H10 RES 1 6.528 7.166 6.093 1.00 20.00
> H
>
> HETATM 1672 H11 RES 1 5.001 5.463 6.872 1.00 20.00
> H
>
> HETATM 1673 C11 RES 1 16.595 7.942 4.799 1.00 20.00
> C
>
> HETATM 1674 1H11 RES 1 16.918 7.013 5.259 1.00 20.00
> H
>
> HETATM 1675 C12 RES 1 15.133 9.868 4.680 1.00 20.00
> C
>
> HETATM 1676 1H12 RES 1 14.282 10.440 5.036 1.00 20.00
> H
>
> HETATM 1677 C13 RES 1 9.715 7.610 7.230 1.00 20.00
> C
>
> HETATM 1678 C14 RES 1 16.969 9.640 3.114 1.00 20.00
> C
>
> HETATM 1679 C15 RES 1 9.463 7.489 8.609 1.00 20.00
> C
>
> HETATM 1680 1H15 RES 1 10.252 7.517 9.346 1.00 20.00
> H
>
> HETATM 1681 C16 RES 1 8.638 7.470 6.342 1.00 20.00
> C
>
> HETATM 1682 1H16 RES 1 8.795 7.537 5.270 1.00 20.00
> H
>
> HETATM 1683 C17 RES 1 15.865 10.359 3.602 1.00 20.00
> C
>
> HETATM 1684 1H17 RES 1 15.555 11.300 3.162 1.00 20.00
> H
>
> HETATM 1685 C18 RES 1 17.325 8.437 3.722 1.00 20.00
> C
>
> HETATM 1686 1H18 RES 1 18.182 7.875 3.362 1.00 20.00
> H
>
> HETATM 1687 C19 RES 1 3.262 11.301 4.209 1.00 20.00
> C
>
> HETATM 1688 1H19 RES 1 3.724 12.284 4.083 1.00 20.00
> H
>
> HETATM 1689 2H19 RES 1 2.211 11.456 4.480 1.00 20.00
> H
>
> HETATM 1690 3H19 RES 1 3.344 10.767 3.256 1.00 20.00
> H
>
> HETATM 1691 O2 RES 1 4.872 8.169 9.151 1.00 20.00
> O
>
> HETATM 1692 S2 RES 1 12.780 7.491 8.731 1.00 20.00
> S
>
> HETATM 1693 N2 RES 1 13.300 8.199 6.275 1.00 20.00
> N
>
> HETATM 1694 C2 RES 1 14.684 8.166 6.442 1.00 20.00
> C
>
> HETATM 1695 C20 RES 1 17.254 11.057 1.187 1.00 20.00
> C
>
> HETATM 1696 1H20 RES 1 17.902 11.224 0.320 1.00 20.00
> H
>
> HETATM 1697 2H20 RES 1 17.223 11.986 1.763 1.00 20.00
> H
>
> HETATM 1698 3H20 RES 1 16.230 10.823 0.877 1.00 20.00
> H
>
> HETATM 1699 H21 RES 1 12.950 8.558 5.392 1.00 20.00
> H
>
> HETATM 1700 C3 RES 1 3.843 7.207 6.512 1.00 20.00
> C
>
> HETATM 1701 N3 RES 1 2.724 6.715 5.928 1.00 20.00
> N
>
> HETATM 1702 O3 RES 1 15.282 7.806 7.449 1.00 20.00
> O
>
> HETATM 1703 N4 RES 1 2.374 8.860 4.878 1.00 20.00
> N
>
> HETATM 1704 O4 RES 1 3.967 10.609 5.251 1.00 20.00
> O
>
> HETATM 1705 C4 RES 1 7.117 7.174 8.177 1.00 20.00
> C
>
> HETATM 1706 C5 RES 1 4.301 8.505 6.294 1.00 20.00
> C
>
> HETATM 1707 N5 RES 1 10.998 7.821 6.637 1.00 20.00
> N
>
> HETATM 1708 O5 RES 1 17.784 10.029 2.038 1.00 20.00
> O
>
> HETATM 1709 H51 RES 1 5.214 8.880 6.746 1.00 20.00
> H
>
> HETATM 1710 C6 RES 1 3.516 9.301 5.465 1.00 20.00
> C
>
> HETATM 1711 C7 RES 1 2.045 7.580 5.146 1.00 20.00
> C
>
> HETATM 1712 H71 RES 1 1.139 7.204 4.682 1.00 20.00
> H
>
> HETATM 1713 C8 RES 1 15.486 8.652 5.279 1.00 20.00
> C
>
> HETATM 1714 C9 RES 1 8.172 7.275 9.083 1.00 20.00
> C
>
> HETATM 1715 H91 RES 1 8.011 7.185 10.152 1.00 20.00
> H
>
> END
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Received on Tue May 13 2014 - 04:00:07 PDT
