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
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>>> 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)
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Received on Fri Apr 29 2016 - 09:30:04 PDT
