[gmx-users] Can not write a pdb file without atom names (concatenating 2 pdb files)

[Mark Abraham]

Hi,

PDB format needs atom names but trjcat only knows how to read those from a
-s input file.

Mark

On Thu, 3 Aug 2017 08:34 Andrew Bostick <andrew.bostick1 at gmail.com> wrote:

> Dear gromacs users,
>
> I have 2 trajectory files as pdb format.
>
> I want to have only one file using the following command:
>
> gmx_mpi trjcat -f 9_ms.pdb 19.pdb -o mix.pdb -settime
>
> I encountered with:
>
> ---------------------------------------------------------------------
>
> Command line:
>   gmx_mpi trjcat -f 9_ms.pdb 19.pdb -o mix.pdb -settime
>
> Reading frame       0 time    0.000    'c15 t= 30000.00000', 6250 atoms
> Reading frame       0 time    0.000    'c15 t= 30000.00000', 6250 atoms
> Reading frame       1 time 30000.000
>
>
> Enter the new start time (ps) for each file.
> There are two special options, both disable sorting:
>
> c (continue) - The start time is taken from the end
> of the previous file. Use it when your continuation run
> restarts with t=0.
>
> l (last) - The time in this file will be changed the
> same amount as in the previous. Use it when the time in the
> new run continues from the end of the previous one,
> since this takes possible overlap into account.
>
>           File             Current start (ps)  New start (ps)
> ---------------------------------------------------------
>                  9_ms.pdb        0.000 ps          0
>                    19.pdb        0.000 ps          9000000
>
> Summary of files and start times used:
>
>           File                Start time       Time step
> ---------------------------------------------------------
>                  9_ms.pdb        0.000 ps    30000.000 ps
>                    19.pdb   9000000.000 ps    30000.000 ps
>
>
> Back Off! I just backed up mix.pdb to ./#mix.pdb.4#
> Reading frame       0 time    0.000
>
> Continue writing frames from 9_ms.pdb t=0 ps, frame=0
>
> -------------------------------------------------------
> Program gmx trjcat, VERSION 5.1.3
> Source code file:
> /root/gromacs_source/gromacs-5.1.3/src/gromacs/fileio/trxio.c, line: 557
>
> Fatal error:
> Can not write a pdb file without atom names
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> -----------------------------------------------------------------------
>
> How to resolve this issue?
>
> Best,
> Andrew
> --
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