On Tue, May 13, 2014 at 12:44 AM, Biao Ma <jackyma1981.gmail.com> wrote:
> Hi, amber users.
>
> when I perform antechamber (Amber12, AmberTools13), I got the follow errors.
In general, it is recommended that you update to the latest version of
AmberTools (currently 14).
-Dan
>
>
> 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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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue May 13 2014 - 11:00:09 PDT
