Dear Amber users,
I am trying to use antechamber to create parameter and coordinate files for
my molecule. Then I run "antechamber -i input.pdb -fi pdb -o output.mol2 -fo
mol2 -c bcc -s 2". The job was aborted after running 130 hours and I got the
error message as follow:
Total number of electrons: 910; net charge: 0
Running: /share/apps/amber11/bin/sqm -O -i sqm.in -o sqm.out
*** glibc detected *** antechamber: free(): invalid next size (normal):
0x000000000da83060 ***
======= Backtrace: =========
/lib64/libc.so.6[0x3e89a722ef]
/lib64/libc.so.6(cfree+0x4b)[0x3e89a7273b]
/lib64/libc.so.6(fclose+0x14b)[0x3e89a60d5b]
antechamber[0x416ac0]
antechamber[0x4062e4]
/lib64/libc.so.6(__libc_start_main+0xf4)[0x3e89a1d994]
antechamber[0x4011d9]
======= Memory map: ========
00400000-0044e000 r-xp 00000000 00:1b 19662478
/share/apps/amber11/bin/antechamber
0064e000-0064f000 rwxp 0004e000 00:1b 19662478
/share/apps/amber11/bin/antechamber
0064f000-00661000 rwxp 0064f000 00:00 0
0da6b000-0da9d000 rwxp 0da6b000 00:00 0
[heap]
3e89600000-3e8961c000 r-xp 00000000 08:01 423489
/lib64/ld-2.5.so
3e8981b000-3e8981c000 r-xp 0001b000 08:01 423489
/lib64/ld-2.5.so
3e8981c000-3e8981d000 rwxp 0001c000 08:01 423489
/lib64/ld-2.5.so
3e89a00000-3e89b4d000 r-xp 00000000 08:01 423490
/lib64/libc-2.5.so
3e89b4d000-3e89d4d000 ---p 0014d000 08:01 423490
/lib64/libc-2.5.so
3e89d4d000-3e89d51000 r-xp 0014d000 08:01 423490
/lib64/libc-2.5.so
3e89d51000-3e89d52000 rwxp 00151000 08:01 423490
/lib64/libc-2.5.so
3e89d52000-3e89d57000 rwxp 3e89d52000 00:00 0
3e89e00000-3e89e02000 r-xp 00000000 08:01 423125
/lib64/libdl-2.5.so
3e89e02000-3e8a002000 ---p 00002000 08:01 423125
/lib64/libdl-2.5.so
3e8a002000-3e8a003000 r-xp 00002000 08:01 423125
/lib64/libdl-2.5.so
3e8a003000-3e8a004000 rwxp 00003000 08:01 423125
/lib64/libdl-2.5.so
3e8a600000-3e8a682000 r-xp 00000000 08:01 423497
/lib64/libm-2.5.so
3e8a682000-3e8a881000 ---p 00082000 08:01 423497
/lib64/libm-2.5.so
3e8a881000-3e8a882000 r-xp 00081000 08:01 423497
/lib64/libm-2.5.so
3e8a882000-3e8a883000 rwxp 00082000 08:01 423497
/lib64/libm-2.5.so
3e8be00000-3e8be0d000 r-xp 00000000 08:01 423498
/lib64/libgcc_s-4.1.2-20080825.so.1
3e8be0d000-3e8c00d000 ---p 0000d000 08:01 423498
/lib64/libgcc_s-4.1.2-20080825.so.1
3e8c00d000-3e8c00e000 rwxp 0000d000 08:01 423498
/lib64/libgcc_s-4.1.2-20080825.so.1
2b036d332000-2b036d334000 rwxp 2b036d332000 00:00 0
2b036d334000-2b036d591000 r-xp 00000000 00:1b 21959984
/share/apps/intel/cce/10.1.015/lib/libimf.so
2b036d591000-2b036d691000 ---p 0025d000 00:1b 21959984
/share/apps/intel/cce/10.1.015/lib/libimf.so
2b036d691000-2b036d695000 rwxp 0025d000 00:1b 21959984
/share/apps/intel/cce/10.1.015/lib/libimf.so
2b036d695000-2b036d697000 rwxp 2b036d695000 00:00 0
2b036d6a1000-2b036d6a4000 rwxp 2b036d6a1000 00:00 0
7fff36162000-7fff36186000 rwxp 7ffffffdb000 00:00 0
[stack]
ffffffffff600000-ffffffffffe00000 ---p 00000000 00:00 0
[vdso] <scorpian.susu.gmail.com>
And then I searched online and found it was maybe the memory problem and
something about intel. But I don't know how to fix it. So what should I do
now? Thank you very much and hope for your reply.
Yours sincerely,
Guoxiong Su
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Received on Thu Aug 05 2010 - 11:30:05 PDT
