Re: [AMBER] ambpdb problem with binary restart file. .

From: Date, Mihir <Mihir.Date.STJUDE.ORG>
Date: Wed, 13 Nov 2013 13:38:39 -0600

Thanks Daniel and Jason,
I tried both of the options of direct conversion of rst to pdb and from rst to ascii.rst7 and then to pdb.
Both times I get following error

CPPTRAJ: Trajectory Analysis. V12.5
    ___ ___ ___ ___
     | \/ | \/ | \/ |

  Unrecognized input on command line: 3: -y
Usage: cpptraj [-p <Top1>, -p <Top2>, ...] [-i <Input>] [-debug <N>]
       cpptraj <Top1> <Input>
       Additional options:
         --help, -help: print usage information and exit.
         -V, --version: print version information and exit.
             --defines: print list of defines used in compilation.


From: Daniel Roe []
Sent: Wednesday, November 13, 2013 1:14 PM
To: AMBER Mailing List
Subject: Re: [AMBER] ambpdb problem with binary restart file. .


The restart file is actually a NetCDF restart (ntxo=2), not a raw
binary restart (which is now an obsolete format). I don't think ambpdb
is set up to read NetCDF restart files yet. You can either directly
convert the restart to pdb using cpptraj (V13.X), e.g.

cpptraj -p complex-tip3.prmtop -y prod-NVT-20ns.rst -x prod-NVT-20ns.pdb

or convert from NetCDF restart to ASCII restart and then use ambpdb:

cpptraj -p complex-tip3.prmtop -y prod-NVT-20ns.rst -x
ambpdb -p complex-tip3.prmtop < > prod-NVT-20ns.pdb

Hope this helps,


On Wed, Nov 13, 2013 at 11:43 AM, Date, Mihir <> wrote:
> Hi
> I have production run of my system which was generated using netcdf binary format for trajectory as well as binary format for restart files (using ntxo = 2).
> I am trying to get a pdb file from restart file using following command
> $ ambpdb -bin -p complex-tip3.prmtop < prod-NVT-20ns.rst > prod-NVT-20ns.pdb
> and I get following error message.
> | New format PARM file being parsed.
> | Version = 1.000 Date = 11/08/13 Time = 12:25:34
> At line 889 of file ambpdb.F90 (unit = 5, file = 'stdin')
> Fortran runtime error: Missing format for FORMATTED data transfer
> I checked line 889 of ambpdb.F90 and it seems there is something wrong/unreadable with the title of my binary restart file. (?? you can also correct me if this is not right)
> Can someone give me possible solution on it.
> I have long runs of MD (more than 50ns). I am using the binary format for trajectory as well as restart file so as to avoid character limit problem in these files and avoid post-processing for re-centring.
> Thanks in advance
> Mihir
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Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Nov 13 2013 - 12:00:03 PST
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