[gmx-users] pdb-files - atom number of individual molecules

B. Nick ANick at t-online.de
Thu Jan 29 16:14:01 CET 2004

Dear Gromacs-user,

I am simulating a system of 16 chains. When I write the
final coordinates of the system in pdb-format using
> mdrun -c last.pdb
the sixt column does always equal the second, which means
that the atom number for the single chains (listet in
colum six) is not reseted to 1 when switching from 
molecule A to B and so on. 
This causes problems when I try to read the pdb-files
in other software-programs (i.e. Accelrys will not
detect different molecules and sticks all 16 chains
together to one chain).

Is there a way to prevent this or can I reconvert the files
to "real" pdb using existing tools?
(I already tried trjconv 
> trjconv -f last.pdb -o test.pdb
but this does not change the situation.)

Thanks for any suggestions,

PS: GROMACS itself does recognize the different chains, when
starting consecutive jobs. Does it get the information from
the chain identifier in column 5 of pdb-files? 
If yes, how can I increase the number of different molecules in 
my system beyond 26?

Dr. Birgitta Nick
Lab. of Non-Metallic Materials,
UPM, Spain

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