What happens if you use cpptraj instead of ptraj? With the exception of 1
or 2 commands (found in the manual), it does everything ptraj does and a
bit more.
You can run exactly the same command you did with ptraj, just replace the
ptraj command with cpptraj. You should also tell us what version of
AmberTools you are using (and I suggest upgrading to the newest version,
AmberTools 13).
Good luck,
Jason
On Mon, May 6, 2013 at 3:26 AM, KAMAKSHI SHARMA <kamakshi3010.gmail.com>wrote:
> Dear Amber users
>
> I wanted to calculate dihedral phi,psi angle on output trajectory file of
> PDB structure using ptraj but I am getting the error of *segmentation
> fault*.
> It is not masking any atom post the 29th residue.
>
> On using the same input in the extended structure built using tleap ptraj
> seemed to work fine giving all the dihedral angles.
>
> I am unable to understand the reason for such a discrepancy. the atom types
> of both the files seemed fine.
>
>
> Please find the topology file for linear extended structure
> (cathnew.prmtop)
> and for the PDB structure (cath.prmtop) and also the ptraj input file as an
> attachment with this mail.
>
> if u can help me , i will be grateful
>
> Best wishes
> Kamakshi
>
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>
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon May 06 2013 - 06:00:05 PDT
