HI Dan,
Thanks for your reply. .crd is the coordinate file that I got from H++. I
followed your suggestions and I am still getting errors. Can I use Parmed?
Weird thing is I prepared all the PDBs until now using the same method and
I never had problem. It just started recently.
ambpdb -p complex.top -c complex.crd > new2.pdb
| ambpdb (C++) Version V15.00
Error: AmberRestart::setupTrajin(): Error reading coordinates.
Error: Could not set up h27r.crd for reading.
Any suggestions?
Thank you,
AP
On Fri, Apr 29, 2016 at 10:21 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org <javascript:;>
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> -------------------------
> 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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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Apr 29 2016 - 08:30:06 PDT
