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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>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>> >
>>
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Received on Mon Sep 05 2011 - 17:30:05 PDT
