Hello,
In ptraj.in you have .....
dihedral phi_36 :37.C :38.N :38.CA :38.C out phi_0036
dihedral psi_36 :38.N :38.CA :38.C :39.N out psi_0036
But there are only 37 residues in the pdb file. There wont be any atom
detected for :38.N :38.CA :38.C :38.N :38.CA :38.C :39.N
HTH
/S
On Mon, Jun 3, 2013 at 1:14 PM, parul sharma <sharmaparul7373.gmail.com>wrote:
> Dear Amber users,
>
> I wanted to calculate the dihedral angles (phi. psi, omega) for my
> trajectory obtained using NMR structure. The prmtop was obtained using
> leap, giving pdb as input structure. When i was trying to run the ptraj
> command , its giving segmentation fault, the ptraj.out file was viewed. It
> is unable to mask all the atoms. the pdb and prmtop file (created from the
> pdb structure) are attached. Also the ptraj input and output files are
> attached. I am unable to troubleshoot this for quite some time now. I
> would be grateful if anyone can help me out with this
>
> Thanks in advance
>
> Regards
> Parul Sharma
> *
> *
> *
> *
> --
> Parul Sharma
> RA, Department of Biophysics,
> AIIMS, New Delhi, India.
> Mobile No. +919555676944
>
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Received on Mon Jun 03 2013 - 06:00:04 PDT
