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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Received on Mon Sep 12 2011 - 06:00:02 PDT
