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)
_______________________________________________
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http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Apr 29 2016 - 09:30:03 PDT
