Hi,
Ptraj should be run as:
ptraj <topology> <input>
Did you specify a topology file as the first argument to ptraj?
-Dan
On Wed, Nov 16, 2011 at 6:05 AM, Fernando Blanco <mdgamber.gmail.com> wrote:
> Hello
>
> I am running a MMPBSA tutorial with one Protein-Ligand complex
>
> after the production of dynamics step
> I am trying to run ptraj to obtain the rmsd values of my system
>
> but I get this error
>
> ------------
>
>
> \-/
> -/- PTRAJ: a utility for processing trajectory files
> /-\
> \-/ Version: "AMBER 11.0 integrated" (4/2010)
> -/- Executable is: "ptraj"
> /-\ Running on 1 processor(s)
> \-/ Error scanning a value: parm->NTOTAT
> Error scanning a value: parm->NTYPES
> Error scanning a value: parm->NBONH
> Error scanning a value: parm->NBONA
> Error scanning a value: parm->NTHETH
> Error scanning a value: parm->NTHETA
> Error scanning a value: parm->NPHIH
> Error scanning a value: parm->NPHIA
> Error scanning a value: parm->JHPARM
> Error scanning a value: parm->JPARM
> Error scanning a value: parm->NEXT
> Error scanning a value: parm->NTOTRS
> Error scanning a value: parm->MBONA
> Error scanning a value: parm->MTHETS
> Error scanning a value: parm->MPHIA
> Error scanning a value: parm->MUMBND
> Error scanning a value: parm->MUMANG
> Error scanning a value: parm->MPTRA
> Error scanning a value: parm->NATYP
> Error scanning a value: parm->NHB
> Error scanning a value: parm->IFPERT
> Error scanning a value: parm->NBPER
> Error scanning a value: parm->NGPER
> Error scanning a value: parm->NDPER
> Error scanning a line of 12I6: parm->MBPER
> Error scanning a value: parm->MBPER
> Error scanning a value: parm->MGPER
> Error scanning a value: parm->MDPER
> Error scanning a value: parm->IFBOX
> Error scanning a value: parm->NMXRS
> Error scanning a value: parm->IFCAP
>
> ERROR in NAME_COPY: ... EOF encounters on scanning igraph
>
> ------------
>
> This is my ptraj input file
>
> ----------
>
> trajin ARDHTs_dyn3.mdcrd 1 250 1
> reference ARDHTs.inpcrd
> rms reference out ARDHTs_equil.rmsd .CA,C,N
>
> --------------
>
>
> Thanks in advance if anybody can help me
>
>
> --
> Fernando Blanco
>
> Postdoctoral Researcher
> *Molecular Design Group (MDG)*
> *School of Biochemistry and Immunology*
> *Biomedical Science Institute*
> *Trinity College Dublin*
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe, PhD
Postdoctoral Associate
BioMaPS Institute, Rutgers University
610 Taylor Road
Piscataway, NJ 08854
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Received on Wed Nov 16 2011 - 05:30:05 PST
