Hi,
On Fri, Apr 29, 2016 at 11:01 AM, Arati Paudyal <apsilwal123.gmail.com> wrote:
> 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.
Text files are typically filled with hidden characters called control
characters; these are things like tab, newline, etc. When you see a
line in a text file like:
The quick brown fox
jumped over the lazy dog
It really looks something like this
The quick brown fox\n
jumped over the lazy dog\n
The '\n' represents the hidden control character "newline", which
indicates a new line should start. The problem with 'complex_crd.crd'
is that it is missing that last newline character. If you open it up
in a text editor like 'vim' it let's you know this:
"../complex_crd.crd" [noeol][dos] 1979L, 146309C
The "noeol" means "no end of line", i.e. you are missing a terminal newline.
The end result is that when cpptraj reads in the coordinates it looks
like not enough data has been read in because of the missing character
and it throws an error. I'm modifying cpptraj to handle cases where
the terminal newline is missing in Amber restart files.
Hopefully this clears things up.
> 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.
When you add the line you will in effect be adding that missing
newline. Even when you remove the extra line the newline in your final
line will remain. Typically the only times you end up with a file that
is missing terminal newlines is due to bugs or disk errors etc.
-Dan
>
> 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
>>
>>
> _______________________________________________
> 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)
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Received on Fri Apr 29 2016 - 10:30:05 PDT
