Hello,
I think I found the error reason.
When I generated prmtop sequence from tleap, I didn't specified N and
C terminal. I used GNY and GLU instead of NGLY and CGLU.
I reran my remd and did the same analysis script and it gave me no error.
I guess the error occurs when ptraj treats the kind of absence of
terminal atoms.
Thank you.
Bongkeun Kim
Quoting Daniel Roe <daniel.r.roe.gmail.com>:
> 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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>>>>>>
>>>>>
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Received on Thu Jun 09 2011 - 11:30:02 PDT
