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 - 00:00:04 PDT
