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.
Regards,
Mihir
________________________________________
From: Daniel Roe [daniel.r.roe.gmail.com]
Sent: Wednesday, November 13, 2013 1:14 PM
To: AMBER Mailing List
Subject: Re: [AMBER] ambpdb problem with binary restart file. .
Hi,
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 ascii.prod-NVT-20ns.rst7
ambpdb -p complex-tip3.prmtop < ascii.prod-NVT-20ns.rst7 > prod-NVT-20ns.pdb
Hope this helps,
-Dan
On Wed, Nov 13, 2013 at 11:43 AM, Date, Mihir <Mihir.Date.stjude.org> 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
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Nov 13 2013 - 12:00:03 PST
