Hi,
As I mentioned earlier, you need to use cpptraj version 13. You can
get an updated version of AmberTools here:
http://ambermd.org/AmberTools-get.html. Instructions for installing
AmberTools 13 alongside older Amber distributions can be found in the
manual and over on Jason's wiki:
http://jswails.wikidot.com/installing-amber12-and-ambertools-13
-Dan
On Wed, Nov 13, 2013 at 12:38 PM, Date, Mihir <Mihir.Date.stjude.org> wrote:
> 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
>>
>> Email Disclaimer: www.stjude.org/emaildisclaimer
>> Consultation Disclaimer: www.stjude.org/consultationdisclaimer
>>
>>
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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 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
> _______________________________________________
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> 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 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
