Hi,
I'm not able to reproduce the error. I'm using a 1000 frame trajectory
and topology file built from the PDB you sent me (minus the extra H).
How large was the trajectory you are trying to process? Can you send
me the topology file you are using?
-Dan
On Thu, Jun 9, 2011 at 3:49 AM, Bongkeun Kim <bkim.chem.ucsb.edu> wrote:
> Hello,
>
> I deleted that extra H atom (it may came from cutting in VMD) and ran
> a script again. It still gave me the same error.
> Thank you,.
> Bongkeun Kim
>
> Quoting Daniel Roe <daniel.r.roe.gmail.com>:
>
>> 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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>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>
>>>>
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Received on Thu Jun 09 2011 - 10:30:03 PDT
