Thanks Junjun and Dan,
Today, I try to update AmberTools,
first, I do the following work, I got some error when run ./update_amber
--check-updates.
I think that no effect on next process, and I did the next process,
to run "# ./update_amber -update" and type "Yes" to download the update
files.
then, I try to re-run " ./configure intel", but failed the error info is
following.
who can tell me is where wrong?
thank you,
Biao
==================
cd $AMBERHOME
su root
./update_amber -v
Version is reported as <version>.<patches applied>
AmberTools version 13.00
Amber version 12.15
./update_amber --check-updates
Checking for available patches online. This may take a few seconds...
Available AmberTools 13 patches:
update.1, update.2, update.3, update.4, update.5, update.6, update.7,
update.8, update.9, update.10,
update.11, update.12, update.13, update.14, update.15, update.16,
update.17, update.18, update.19, update.20,
update.21, update.22, update.23, update.24
Traceback (most recent call last):
File "./update_amber", line 23, in <module>
app.mainloop()
File "/usr/local/amber12/updateutils/main.py", line 467, in mainloop
self.check_updates()
File "/usr/local/amber12/updateutils/main.py", line 175, in check_updates
self.verbose) + '\n')
File "/usr/local/amber12/updateutils/repos.py", line 185, in patch_details
return PatchRepository.patch_details(self, first, verbose)
File "/usr/local/amber12/updateutils/repos.py", line 59, in patch_details
progs = self.patch_list.programs(i)
File "/usr/local/amber12/updateutils/patchlist.py", line 237, in programs
return self._info_wrapper(idx, 'programs')
File "/usr/local/amber12/updateutils/patchlist.py", line 355, in
_info_wrapper
return getattr(self._instantiate(idx), attr)()
File "/usr/local/amber12/updateutils/downloader.py", line 98, in new_fcn
return fcn(*args, **kwargs)
File "/usr/local/amber12/updateutils/patchlist.py", line 337, in
_instantiate
self.sizere.findall(urlopen(self.names[idx]).info())[0])
TypeError: expected string or buffer
=======================================
# ./configure intel
Checking for updates... Checking for available patches online. This may
take a few seconds... Available AmberTools 13 patches: update.1, update.2,
update.3, update.4, update.5, update.6, update.7, update.8, update.9,
update.10, update.11, update.12, update.13, update.14, update.15,
update.16, update.17, update.18, update.19, update.20, update.21,
update.22, update.23, update.24 Traceback (most recent call last): File
"./update_amber", line 23, in <module> app.mainloop() File
"/usr/local/amber12/updateutils/main.py", line 467, in mainloop
self.check_updates() File "/usr/local/amber12/updateutils/main.py", line
175, in check_updates self.verbose) + '\n') File
"/usr/local/amber12/updateutils/repos.py", line 185, in patch_details
return PatchRepository.patch_details(self, first, verbose) File
"/usr/local/amber12/updateutils/repos.py", line 59, in patch_details progs
= self.patch_list.programs(i) File
"/usr/local/amber12/updateutils/patchlist.py", line 237, in programs return
self._info_wrapper(idx, 'programs') File
"/usr/local/amber12/updateutils/patchlist.py", line 355, in _info_wrapper
return getattr(self._instantiate(idx), attr)() File
"/usr/local/amber12/updateutils/downloader.py", line 98, in new_fcn return
fcn(*args, **kwargs) File "/usr/local/amber12/updateutils/patchlist.py",
line 337, in _instantiate
self.sizere.findall(urlopen(self.names[idx]).info())[0]) TypeError:
expected string or buffer Check for updates failed. Detected icc version 11
Detected ifort version 11 Testing the icc compiler: icc
-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c OK Testing the
ifort compiler: ifort -O0 -o testp testp.f OK Testing mixed C/Fortran
compilation: icc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -c -o testp.c.o
testp.c ifort -O0 -c -o testp.f.o testp.f icc -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -o testp testp.c.o testp.f.o
-L/opt/intel/Compiler/11.1/080/lib/intel64 -lifport -lifcore -lsvml ld:
warning: libimf.so, needed by
/opt/intel/Compiler/11.1/080/lib/intel64/libifport.so.5, not found (try
using -rpath or -rpath-link) ld: warning: libintlc.so.5, needed by
/opt/intel/Compiler/11.1/080/lib/intel64/libifport.so.5, not found (try
using -rpath or -rpath-link) ld: testp: hidden symbol
`__intel_cpu_indicator_init' in
/opt/intel/Compiler/11.1/080/lib/intel64/libirc.a(cpu_disp.o) is referenced
by DSO ld: final link failed: Nonrepresentable section on output
./configure2: line 1786: ./testp: No such file or directory Error: Unable
to compile mixed C/Fortran code. Please check your compiler settings and
configure flags. Configure failed due to the errors above!
On Wed, May 14, 2014 at 2:36 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> 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)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed May 14 2014 - 07:30:03 PDT
