AMBER Archive (2008)

Subject: Re: AMBER: xleap fails to savemol2

From: taufik.alsarraj_at_utoronto.ca
Date: Fri Aug 29 2008 - 12:28:33 CDT

Hi Francois,
Thank you for the suggestions. Unfortunately xleap and tlean still
crashes. I am attaching the new surface file - i am still using the
same script.

the output file before crashing contains this
@<TRIPOS>MOLECULE
SiO2_quartz
   890 970 1 0 1
SMALL
USER_CHARGES
@<TRIPOS>ATOM
   1 O1 1.760000 0.299000 1.157000 O 1 SiO2
  -0.8000 ****

--So one line is written only

The message from tleap is
> savemol2 sur surfacefran2.mol2 0
Writing mol2 file: surfacefran2.mol2
*** stack smashing detected ***:
/home/taufik/lab/amber-10.07/bin/teLeap terminated
======= Backtrace: =========
/lib/tls/i686/cmov/libc.so.6(__fortify_fail+0x48)[0xb7f44138]
/lib/tls/i686/cmov/libc.so.6(__fortify_fail+0x0)[0xb7f440f0]
/home/taufik/lab/amber-10.07/bin/teLeap[0x8054a1a]
/home/taufik/lab/amber-10.07/bin/teLeap[0x80a98cd]
/home/taufik/lab/amber-10.07/bin/teLeap[0x80a9a40]
/home/taufik/lab/amber-10.07/bin/teLeap[0x80a9e41]
/home/taufik/lab/amber-10.07/bin/teLeap[0x80b884b]
/home/taufik/lab/amber-10.07/bin/teLeap[0x80af41b]
/home/taufik/lab/amber-10.07/bin/teLeap[0x80b10e6]
/home/taufik/lab/amber-10.07/bin/teLeap[0x80c5549]
/lib/tls/i686/cmov/libc.so.6(__libc_start_main+0xe0)[0xb7e6d450]
/home/taufik/lab/amber-10.07/bin/teLeap[0x8049531]
======= Memory map: ========
08048000-080df000 r-xp 00000000 07:00 32371
/home/taufik/lab/amber-10.07/bin/teLeap
080df000-080fd000 rw-p 00096000 07:00 32371
/home/taufik/lab/amber-10.07/bin/teLeap
080fd000-08d5f000 rw-p 080fd000 00:00 0 [heap]
b7e56000-b7e57000 rw-p b7e56000 00:00 0
b7e57000-b7fa0000 r-xp 00000000 07:00 267352
/lib/tls/i686/cmov/libc-2.7.so
b7fa0000-b7fa1000 r--p 00149000 07:00 267352
/lib/tls/i686/cmov/libc-2.7.so
b7fa1000-b7fa3000 rw-p 0014a000 07:00 267352
/lib/tls/i686/cmov/libc-2.7.so
b7fa3000-b7fa6000 rw-p b7fa3000 00:00 0
b7fa6000-b7fc9000 r-xp 00000000 07:00 267360
/lib/tls/i686/cmov/libm-2.7.so
b7fc9000-b7fcb000 rw-p 00023000 07:00 267360
/lib/tls/i686/cmov/libm-2.7.so
b7fcb000-b7fd5000 r-xp 00000000 07:00 250048 /lib/libgcc_s.so.1
b7fd5000-b7fd6000 rw-p 0000a000 07:00 250048 /lib/libgcc_s.so.1
b7fd6000-b7fda000 rw-p b7fd6000 00:00 0
b7fda000-b7fdb000 r-xp b7fda000 00:00 0 [vdso]
b7fdb000-b7ff5000 r-xp 00000000 07:00 250003 /lib/ld-2.7.so
b7ff5000-b7ff7000 rw-p 00019000 07:00 250003 /lib/ld-2.7.so
bfb8c000-bfbcc000 rw-p bffc0000 00:00 0 [stack]
Aborted

Not sure what that means,
Taufik

Quoting FyD <fyd_at_q4md-forcefieldtools.org>:

> Quoting taufik.alsarraj_at_utoronto.ca:
>
>> i have a mol2 file, i can read it just fine with xleap and i can also
>> convert it to *.prmtop and *.inpcrd. However i cannot savemol2.
>>
>> my script:
>> source leaprc.ff99SB
>> source leaprc.gaff
>> loadamberparams mysioforce.frcmod
>> sur = loadmol2 "newsurface.mol2"
>> check sur
>> saveamberparm surfacealone.prmtop surfacealone.inpcrd
>> savepdb sur surface.pdb
>> savemol2 sur surface0.mol2 0
>> savemol2 sur surface1.mol2 1
>> solvatebox sur TIP3PBOX 8.0
>> saveamberparm surfacesolvent.prmtop surfacesolvent.inpcrd
>> edit sur
>>
>> i attached mysioforce.frcmod and newsurface.mol2
>> savepdb fails and savemol2 (0 and 1) causes xleap to crash.
>>
>> Any suggestions?,
>
> I did not test with Amber10 yet, but with Amber8 + source files
> available from http://q4md-forcefieldtools.org/Tutorial/leap.php.
>
> I am not sure your Tripos mol2 file format is correct in your input
> structure.
> See the official description of this file format:
> http://www.tripos.com/index.php?family=modules,SimplePage,,,&page=sup_mol2&s=0
> & for a simple example, see:
> http://q4md-forcefieldtools.org/REDDB/up/W-1/tripos1.mol2
>
> In particular in your mol2 file:
> 1) the "number of residue" is not present:
> 890 970
> =>
> 890 970 1 0 1
>
> 2) the "substructure" information is empty:
> => add at the end of your file such a line:
> 1 UNK 1 **** 0 **** ****
>
> Does it help ?
>
> regards, Francois
>
>
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