Hi,
Is complex.crd a trajectory file? Try using the -c command line flag to
specify it instead of the redirect, i.e. ambpdb -p complex.top
-c complex.crd > new2.pdb
-Dan
On Friday, April 29, 2016, Arati Paudyal <apsilwal123.gmail.com> wrote:
> Dear experts,
>
> I have been using H++ to prepare any PDB files for simulation. I basically
> take the coordinate and topology files from H++ result and then create a
> new PDB to run for simulation. I basically copy and paste the .crd and .top
> files in new txt files and then run the "ambpdb" command as follows. It
> used to work perfectly until few weeks back. But now when I try to run the
> same PDB files from H++ I get error message in Amber.
>
>
>
> ambpdb -p complex.top < complex.crd > new2.pdb
>
> | ambpdb (C++) Version V15.00
> | Reading Amber restart from STDIN
> Error: AmberRestart::setupTrajin(): When attempting to read in
> Error: box coords/velocity info got 1975 chars, expected 0, 37,
> Error: 73, or 144321.
> Error: This usually indicates a malformed or corrupted restart file.
>
> I used ParmEd as follows and it runs finewith the same .crd and .top files.
> Is there any difference between creating new PDB using "ambpdb" Vs ParmEd?
>
> parmed.py -p complex.top -c complex.crd
> ParmEd: a Parameter file Editor
>
>
> Loaded Amber topology file h27r.top with coordinates from h27r.crd
>
> Reading input from STDIN...
> > outpdb new2.pdb
> Writing PDB file new2.pdb renumbering atoms and residues
> quit
>
>
>
> I would really appreciate your help on this.
>
> AP
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>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Apr 29 2016 - 07:30:02 PDT
