Dan,
Thank you for the file. Please excuse my question again but I literally
don't see any differences between the "fixed" file and the original one
when I open in wordpad. Could you please elaborate a little bit more here.
Adding a line and then removing it again will bring it to the same
situation, right? I think I am not understanding this in detail.
Thanks again for taking your time to fix this.
On Fri, Apr 29, 2016 at 12:17 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> FYI here is the fixed coordinate file.
>
> On Fri, Apr 29, 2016 at 10:16 AM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> > Hi,
> >
> > I received your files. The problem is that 'complex_crd.crd' has no
> > terminal EOL, so when cpptraj reads the coordinates in it appears that
> > there is one less byte than there should be. This is a bug in H++.
> >
> > I'll look into a fix for cpptraj. In the meantime you can work around
> > it by going into the file with an editor, adding a blank line to the
> > end, then removing that line.
> >
> > Thanks for the report,
> >
> > -Dan
> >
> > On Fri, Apr 29, 2016 at 9:27 AM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> >> Can you send me your topology and coordinates off-list so I can try to
> >> reproduce the error? Thanks.
> >>
> >> -Dan
> >>
> >> On Fri, Apr 29, 2016 at 9:25 AM, Arati Paudyal <apsilwal123.gmail.com>
> wrote:
> >>> 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)
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> 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)
> >
> >
> >
> > --
> > -------------------------
> > 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)
>
>
>
> --
> -------------------------
> 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)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Fri Apr 29 2016 - 10:30:03 PDT
