Hi,
There seems to be a problem with the PDB you sent me. The N-terminal
glycine has an extra H (atom number 10) right next to the H1 atom
(atom number 2), and as a result there are 5 bonds to that nitrogen
atom. I'm not sure if this is related to the segfault or not, but I
wanted to bring it to your attention.
-Dan
2011/6/7 Bongkeun Kim <bkim.chem.ucsb.edu>:
> Hello,
>
> I found that this error occurred at the computer that was installed with
> AmberTools 1.5 with bugfix 4. We installed it only on one computer and that
> gives this error.
> I attached the first 10 snapshots from the big traj file and pdb file for
> reference pdb for rms calculation.
> The input script you can use is following;
> ----------------------
> #!/bin/bash
> ptraj beta.prmtop <<EOF
> trajin remd3.Ttraj.273.8.crd
> reference beta2.pdb
> rms reference out rmsr3.273.8.dat :1-16.N,CA,C
> radgyr out rg3.273.8.dat :1-16
> distance d1 :1.CA :16.CA out dist3.273.8.dat
> rms first out rms3.273.8.dat :1-16
> go
> EOF
> --------------------------------
> Thank you.
> Bongkeun Kim
>
>
>
>
> Quoting Daniel Roe <daniel.r.roe.gmail.com>:
>
>> Hi,
>>
>> Since you see this error on one computer only it's possible the
>> problem is with that computer. However, just to be certain could you
>> send me your ptraj input as well as a topology and restart file for
>> your system so I can attempt to reproduce the error? Thanks.
>>
>> -Dan
>>
>> On Mon, Jun 6, 2011 at 4:30 PM, Bongkeun Kim <bkim.chem.ucsb.edu> wrote:
>>>
>>> Dear AMBER,
>>>
>>> I got this error the end of ptraj run.
>>> After this error, mostly I got all the outputs without any problem.
>>> But ptraj just stopped in the middle of analysis run.
>>> I have several PCs, they are running Ubuntu 10.04 with nfs file
>>> system, so they have the same softare/hardware setup. But I can see
>>> this error from the only one computer always. Do you think this is
>>> because of hardware failure?
>>> I'm running AMBER 11 and AmberTools 1.4 and applied all the patches
>>> until April.
>>> The error messages are:
>>> ==================================================
>>> PTRAJ RMS: dumping RMSd vs time data
>>> *** glibc detected *** ptraj: free(): invalid next size (normal):
>>> 0x0000000001ecdd70 ***
>>> ======= Backtrace: =========
>>> /lib/libc.so.6(+0x775b6)[0x7f23882515b6]
>>> /lib/libc.so.6(cfree+0x73)[0x7f2388257e83]
>>> ptraj[0x4234f2]
>>> ptraj[0x44c5a9]
>>> ptraj[0x455753]
>>> ptraj[0x439c15]
>>> ptraj[0x402c41]
>>> /lib/libc.so.6(__libc_start_main+0xfd)[0x7f23881f8c4d]
>>> ptraj[0x4027b9]
>>> ======= Memory map: ========
>>> 00400000-0055f000 r-xp 00000000 00:15 301212899
>>> /home/bkim/packages/amber11/bin/ptraj
>>> 0075e000-0075f000 r--p 0015e000 00:15 301212899
>>> /home/bkim/packages/amber11/bin/ptraj
>>> 0075f000-00769000 rw-p 0015f000 00:15 301212899
>>> /home/bkim/packages/amber11/bin/ptraj
>>> 00769000-0076d000 rw-p 00000000 00:00 0
>>> 01eaa000-01f0d000 rw-p 00000000 00:00 0
>>> [heap]
>>> 7f2383de9000-7f2383dff000 r-xp 00000000 09:01 8110
>>> /lib/libgcc_s.so.1
>>> 7f2383dff000-7f2383ffe000 ---p 00016000 09:01 8110
>>> /lib/libgcc_s.so.1
>>> 7f2383ffe000-7f2383fff000 r--p 00015000 09:01 8110
>>> /lib/libgcc_s.so.1
>>> 7f2383fff000-7f2384000000 rw-p 00016000 09:01 8110
>>> /lib/libgcc_s.so.1
>>> 7f2384000000-7f2384021000 rw-p 00000000 00:00 0
>>> 7f2384021000-7f2388000000 ---p 00000000 00:00 0
>>> 7f23881da000-7f2388354000 r-xp 00000000 09:01 8429
>>> /lib/libc-2.11.1.so
>>> 7f2388354000-7f2388553000 ---p 0017a000 09:01 8429
>>> /lib/libc-2.11.1.so
>>> 7f2388553000-7f2388557000 r--p 00179000 09:01 8429
>>> /lib/libc-2.11.1.so
>>> 7f2388557000-7f2388558000 rw-p 0017d000 09:01 8429
>>> /lib/libc-2.11.1.so
>>> 7f2388558000-7f238855d000 rw-p 00000000 00:00 0
>>> 7f238855d000-7f23885df000 r-xp 00000000 09:01 8476
>>> /lib/libm-2.11.1.so
>>> 7f23885df000-7f23887de000 ---p 00082000 09:01 8476
>>> /lib/libm-2.11.1.so
>>> 7f23887de000-7f23887df000 r--p 00081000 09:01 8476
>>> /lib/libm-2.11.1.so
>>> 7f23887df000-7f23887e0000 rw-p 00082000 09:01 8476
>>> /lib/libm-2.11.1.so
>>> 7f23887e0000-7f23888cb000 r-xp 00000000 09:01 8108
>>> /usr/lib/libgfortran.so.3.0.0
>>> 7f23888cb000-7f2388aca000 ---p 000eb000 09:01 8108
>>> /usr/lib/libgfortran.so.3.0.0
>>> 7f2388aca000-7f2388acb000 r--p 000ea000 09:01 8108
>>> /usr/lib/libgfortran.so.3.0.0
>>> 7f2388acb000-7f2388acc000 rw-p 000eb000 09:01 8108
>>> /usr/lib/libgfortran.so.3.0.0
>>> 7f2388acc000-7f2388acd000 rw-p 00000000 00:00 0
>>> 7f2388acd000-7f2388aed000 r-xp 00000000 09:01 6737
>>> /lib/ld-2.11.1.so
>>> 7f2388bc5000-7f2388cc9000 rw-p 00000000 00:00 0
>>> 7f2388ce8000-7f2388cec000 rw-p 00000000 00:00 0
>>> 7f2388cec000-7f2388ced000 r--p 0001f000 09:01 6737
>>> /lib/ld-2.11.1.so
>>> 7f2388ced000-7f2388cee000 rw-p 00020000 09:01 6737
>>> /lib/ld-2.11.1.so
>>> 7f2388cee000-7f2388cef000 rw-p 00000000 00:00 0
>>> 7fff18bed000-7fff18c02000 rw-p 00000000 00:00 0
>>> [stack]
>>> 7fff18d46000-7fff18d47000 r-xp 00000000 00:00 0
>>> [vdso]
>>> ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0
>>> [vsyscall]
>>> ./analyze_all_temps.x: line 5: 1184 Aborted ptraj
>>> beta.prmtop <<EOF
>>> ==============================================
>>> Thank you.
>>> Bongkeun Kim
>>>
>>>
>>>
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>>>
>>
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Received on Wed Jun 08 2011 - 07:30:03 PDT
