Hi Dan,
Thanks for your reply!
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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> >
> >
>
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Received on Mon Sep 05 2011 - 16:30:03 PDT
