Re: [AMBER] ambpdb problem with binary restart file

From: Jason Swails <>
Date: Wed, 13 Nov 2013 14:16:45 -0500

On Wed, 2013-11-13 at 12:43 -0600, 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.

The problem is that ambpdb is old and NetCDF restarts are new. ambpdb
is incapable of reading them, and it may not get added. You can use
cpptraj to convert NetCDF restarts directly to PDB files if you want.
Using the latest version of cpptraj from AmberTools 13, it would look
something like this:

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

The output trajectory (-x) format is determined from the filename
extension. If, however, you need some feature of ambpdb that is not in
cpptraj (like residue name conversions for 'Amber' residue names like
HIP, HIE, HID, etc.), then you need to generate an ASCII restart file
and use that with ambpdb. So something like this:

cpptraj -p complex-tip3.prmtop -y prod-NVT-20ns.rst -x tmp.rst7
ambpdb -p complex-tip3.prmtop < tmp.rst7 > prod-NVT-20ns.pdb
rm tmp.rst7

The 'binary' restart files that ambpdb is referring to another
(deprecated) restart format that hasn't been used since before my time
with Amber.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Wed Nov 13 2013 - 11:30:03 PST
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