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

[Andrew Bostick]

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