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)
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Received on Fri Apr 29 2016 - 08:30:07 PDT
