Dear Dan,
Please find attached the complete output of cpptraj from a run that
segfaults (wt-log) and the details of compilers and their versions.
While configuring Amber , I used the guidelines given in
the manual.
Thanks,
Praapti
On 9/12/11, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> I cannot reproduce your error using a 10 frame trajectory file created
> from the PDB you sent, and valgrind shows no memory errors or leaks
> (see attached output). In order to debug this further I'm going to
> need more information. Can you 1) send me the complete output (stdout
> + stderr) of cpptraj from a run that segfaults, 2) let me know what
> compilers you are using and what version, and 3) let me know what
> flags you specified when configuring Amber. Thanks!
>
> -Dan
>
> On Mon, Sep 12, 2011 at 2:58 AM, Praapti Jayaswal <praapti.gmail.com> wrote:
>> Dear Dan,
>>
>> I applied the new patch (bugfix.16) and reinstalled Amber11. However,
>> segmentation fault persists when i try to calculate rmsd using cpptraj for
>> more than one frame of trajectory, when waters are stripped. I have also
>> tried the above mentioned exercise on other Linux Systems, but the
>> segmentation fault persists.
>>
>> Please suggest a solution!
>>
>> Praapti
>>
>> On Tue, Sep 6, 2011 at 5:56 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>
>>> Hi,
>>>
>>> There is now a patch posted (bugfix.16) that should fix this. Let me
>>> know if the problem is still occurring after applying the patch (make
>>> sure that bugfixes 1-15 have already been applied).
>>>
>>> http://ambermd.org/bugfixesat.html
>>>
>>> -Dan
>>>
>>> On Mon, Sep 5, 2011 at 12:01 AM, Praapti Jayaswal <praapti.gmail.com>
>>> wrote:
>>> > The command works perfectly if :
>>> > (i) I use the entire solvated trajectory for calculating rmsd for more
>>> than
>>> > one frame, or
>>> > (ii) if I calculate rmsd for one frame when waters are stripped.
>>> >
>>> > However, segmentation fault occurs when I try to calculate rmsd using
>>> > cpptraj for more than one frame when waters are stripped.
>>> >
>>> > Praapti
>>> >
>>> >
>>> >
>>> > On Sat, Sep 3, 2011 at 4:00 AM, Daniel Roe <daniel.r.roe.gmail.com>
>>> wrote:
>>> >
>>> >> Hi,
>>> >>
>>> >> I couldn't reproduce this error - however, I notice that your 'range'
>>> >> argument is 1-160, while you only have 154 residues in your topology.
>>> >> I looked at the code and it's possible that this could cause a
>>> >> segfault on some systems. Try this command instead and let me know if
>>> >> the segfault goes away:
>>> >>
>>> >> rmsd :1-154 reference perres range 1-154 perresout back.tmp perresmask
>>> >> .CA,C,O,N
>>> >>
>>> >> In the meantime I will work on a patch.
>>> >>
>>> >> -Dan
>>> >>
>>> >> On Thu, Sep 1, 2011 at 2:02 AM, Praapti Jayaswal <praapti.gmail.com>
>>> >> wrote:
>>> >> > Hi All,
>>> >> >
>>> >> > With reference to the query posted by my colleague, Xiao Chen (
>>> >> > http://archive.ambermd.org/201106/0259.html), I am also getting
>>> >> segmentation
>>> >> > fault , when i run cpptraj to calculate rmsd for the residues using
>>> >> > trajectory (with waters stripped, i.e. wt_dry.mdcrd).
>>> >> >
>>> >> >
>>> >> > trajin wt_dry.mdcrd
>>> >> > reference wt.pdb
>>> >> > rmsd :1-160 reference perres range 1-160 perresout back.tmp
>>> >> > perresmask
>>> >> > .CA,C,O,N
>>> >> > go
>>> >> >
>>> >> > cpptraj wt_dry.prmtop cpptraj_rmsd.in
>>> >> >
>>> >> >
>>> >> >
>>> >> > I have performed bugfix for ambertools 1.5 on
>>> >> > Linux.<http://archive.ambermd.org/201106/0242.html>
>>> >> >
>>> >> > Please find attached the pdb file, since the size of the parameter
>>> >> > and
>>> >> > trajectory files exceeds permissible size limit.
>>> >> >
>>> >> > Could you please help??
>>> >> >
>>> >> > Thanks,
>>> >> >
>>> >> > Praapti
>>> >> >
>>> >> > _______________________________________________
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>>> >> > AMBER.ambermd.org
>>> >> > http://lists.ambermd.org/mailman/listinfo/amber
>>> >> >
>>> >> >
>>> >>
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- application/octet-stream attachment: wt-log
- application/octet-stream attachment: compilers
Received on Mon Sep 12 2011 - 22:00:02 PDT
