AMBER Archive (2008)

Subject: Re: AMBER: xleap fails to savemol2

From: alsarraj (taufik.alsarraj_at_utoronto.ca)
Date: Thu Sep 18 2008 - 15:15:20 CDT

Hi,
I tried again -the two lines of loading and saving mol2, i am using
Intel(R) Pentium(R) 4 CPU 3.00GHz, Ubuntu 8.04

xleap crashes and the out put is below. i think i have to type 'sudo ln
-s /usr/lib/libXt.so.6 /usr/lib/libXt.so' i hope i am close solving this
problem

taufik_at_taufik-desktop:~/Desktop$ -I: Adding
/usr/local/Programs/amber10.08/dat/leap/prep to search path.
-I: Adding /usr/local/Programs/amber10.08/dat/leap/lib to search path.
-I: Adding /usr/local/Programs/amber10.08/dat/leap/parm to search path.
-I: Adding /usr/local/Programs/amber10.08/dat/leap/cmd to search path.
*** stack smashing detected ***:
/usr/local/Programs/amber10.08/bin/xaLeap terminated
======= Backtrace: =========
/lib/tls/i686/cmov/libc.so.6(__fortify_fail+0x48)[0xb7ccd138]
/lib/tls/i686/cmov/libc.so.6(__fortify_fail+0x0)[0xb7ccd0f0]
/usr/local/Programs/amber10.08/bin/xaLeap[0x8058c4a]
/usr/local/Programs/amber10.08/bin/xaLeap[0x80adafd]
/usr/local/Programs/amber10.08/bin/xaLeap[0x80adc70]
/usr/local/Programs/amber10.08/bin/xaLeap[0x80ae071]
/usr/local/Programs/amber10.08/bin/xaLeap[0x80bca7b]
/usr/local/Programs/amber10.08/bin/xaLeap[0x80b364b]
/usr/local/Programs/amber10.08/bin/xaLeap[0x80b5316]
/usr/local/Programs/amber10.08/bin/xaLeap[0x80ddd38]
/usr/local/Programs/amber10.08/bin/xaLeap[0x80df7df]
/usr/lib/libXt.so.6[0xb7ecf4c1]
/usr/lib/libXt.so.6[0xb7ecf89b]
/usr/lib/libXt.so.6(_XtTranslateEvent+0x5e8)[0xb7ecfe98]
/usr/lib/libXt.so.6(XtDispatchEventToWidget+0x4c2)[0xb7ea6672]
/usr/lib/libXt.so.6[0xb7ea6e8a]
/usr/lib/libXt.so.6(XtDispatchEvent+0xc7)[0xb7ea5cf7]
/usr/lib/libXt.so.6(XtAppMainLoop+0x4c)[0xb7ea5eac]
/usr/lib/libXt.so.6(XtMainLoop+0x1f)[0xb7ea5eff]
/usr/local/Programs/amber10.08/bin/xaLeap[0x80d6388]
/lib/tls/i686/cmov/libc.so.6(__libc_start_main+0xe0)[0xb7bf6450]
/usr/local/Programs/amber10.08/bin/xaLeap(XtAddCallbacks+0x1f5)[0x804d761]
======= Memory map: ========
08048000-08166000 r-xp 00000000 08:05 582706
/usr/local/Programs/amber10.08/bin/xaLeap
08166000-0818a000 rw-p 0011d000 08:05 582706
/usr/local/Programs/amber10.08/bin/xaLeap
0818a000-08301000 rw-p 0818a000 00:00 0 [heap]
b7b9a000-b7ba4000 r-xp 00000000 08:05 450624 /lib/libgcc_s.so.1
b7ba4000-b7ba5000 rw-p 0000a000 08:05 450624 /lib/libgcc_s.so.1
b7ba5000-b7ba9000 r-xp 00000000 08:05 189761 /usr/lib/libXfixes.so.3.1.0
b7ba9000-b7baa000 rw-p 00003000 08:05 189761 /usr/lib/libXfixes.so.3.1.0
b7baa000-b7bb1000 r-xp 00000000 08:05 189781
/usr/lib/libXrender.so.1.3.0
b7bb1000-b7bb2000 rw-p 00007000 08:05 189781
/usr/lib/libXrender.so.1.3.0
b7bc0000-b7bc2000 rw-p b7bc0000 00:00 0
b7bc2000-b7bc4000 r-xp 00000000 08:05 468289
/lib/tls/i686/cmov/libdl-2.7.so
b7bc4000-b7bc6000 rw-p 00001000 08:05 468289
/lib/tls/i686/cmov/libdl-2.7.so
b7bc6000-b7bdd000 r-xp 00000000 08:05 190585 /usr/lib/libxcb.so.1.0.0
b7bdd000-b7bde000 rw-p 00016000 08:05 190585 /usr/lib/libxcb.so.1.0.0
b7bde000-b7bdf000 r-xp 00000000 08:05 190583
/usr/lib/libxcb-xlib.so.0.0.0
b7bdf000-b7be0000 rw-p 00000000 08:05 190583
/usr/lib/libxcb-xlib.so.0.0.0
b7be0000-b7d29000 r-xp 00000000 08:05 468283
/lib/tls/i686/cmov/libc-2.7.so
b7d29000-b7d2a000 r--p 00149000 08:05 468283
/lib/tls/i686/cmov/libc-2.7.so
b7d2a000-b7d2c000 rw-p 0014a000 08:05 468283
/lib/tls/i686/cmov/libc-2.7.so
b7d2c000-b7d30000 rw-p b7d2c000 00:00 0
b7d30000-b7d44000 r-xp 00000000 08:05 468309
/lib/tls/i686/cmov/libpthread-2.7.so
b7d44000-b7d46000 rw-p 00013000 08:05 468309
/lib/tls/i686/cmov/libpthread-2.7.so
b7d46000-b7d48000 rw-p b7d46000 00:00 0
b7d48000-b7d6b000 r-xp 00000000 08:05 468291
/lib/tls/i686/cmov/libm-2.7.so
b7d6b000-b7d6d000 rw-p 00023000 08:05 468291
/lib/tls/i686/cmov/libm-2.7.so
b7d6d000-b7d71000 r-xp 00000000 08:05 189755 /usr/lib/libXdmcp.so.6.0.0
b7d71000-b7d72000 rw-p 00003000 08:05 189755 /usr/lib/libXdmcp.so.6.0.0
b7d72000-b7d74000 r-xp 00000000 08:05 189744 /usr/lib/libXau.so.6.0.0
b7d74000-b7d75000 rw-p 00001000 08:05 189744 /usr/lib/libXau.so.6.0.0
b7d75000-b7e59000 r-xp 00000000 08:05 189738 /usr/lib/libX11.so.6.2.0
b7e59000-b7e5c000 rw-p 000e4000 08:05 189738 /usr/lib/libX11.so.6.2.0
b7e5c000-b7e71000 r-xp 00000000 08:05 189708 /usr/lib/libICE.so.6.3.0
b7e71000-b7e72000 rw-p 00014000 08:05 189708 /usr/lib/libICE.so.6.3.0
b7e72000-b7e74000 rw-p b7e72000 00:00 0
b7e74000-b7e7b000 r-xp 00000000 08:05 189732 /usr/lib/libSM.so.6.0.0
b7e7b000-b7e7c000 rw-p 00006000 08:05 189732 /usr/lib/libSM.so.6.0.0
b7e7c000-b7e7d000 rw-p b7e7c000 00:00 0
b7e7d000-b7e8a000 r-xp 00000000 08:05 189759 /usr/Aborted
taufik_at_taufik-desktop:~/Desktop$

FyD wrote:
> Quoting taufik.alsarraj_at_utoronto.ca:
>
> We just compiled Ambertools 1.2 + Amber 10 on CentOS release 5.2
> The "savemol2" (xleap & tleap) command works fine.
>
> May I ask you the operating system + machine + compilers used to
> install the Ambertools 1.2 ?
>
> regards, Francois
>
>
>> Yes xleap crashes
>> out put has one line in the atoms only
>> @<TRIPOS>MOLECULE
>> DMSO
>> 10 9 1 0 1
>> SMALL
>> USER_CHARGES
>> @<TRIPOS>ATOM
>> 1 C1 1.352237 -0.856933 0.225852 C 1 DMSO
>> -0.2897 *
>> ***
>>
>> --that is the end of tripos2.mol2
>>
>>
>> Quoting FyD <fyd_at_q4md-forcefieldtools.org>:
>>
>>> Quoting taufik.alsarraj_at_utoronto.ca:
>>>
>>>> Thank you for the suggestions. Unfortunately xleap and tlean still
>>>> crashes.
>>>
>>> We will have Amber10 installed pretty soon: We will test this...
>>>
>>> Using the more basic Tripos mol2 file available @
>>> http://q4md-forcefieldtools.org/REDDB/up/W-1/tripos1.mol2
>>> may I ask you to run this simple script:
>>>
>>> TEST = loadmol2 tripos1.mol2
>>> savemol2 TEST tripos2.mol2 0
>>>
>>> Does it crash also ?
>>>
>>> regards, Francois
>
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