[gmx-users] Re: Re: trjconv and missing chain identifier

Una Bjarnadottir una.bjarnadottir at ucd.ie
Mon Mar 5 11:06:19 CET 2007


Hi Mark and other users, 

Thanks for your reply and apologies for my English.

If the chain identifiers are  discarded by gromacs why do I than get
from trjconv an output file looking like this when having more than one
chain in the .trr file like in this example (part of .pdb file)

ATOM   2776  O1  PHE A 336      32.109  64.621  29.258  1.00  0.00
ATOM   2777  O2  PHE A 336      30.372  64.241  30.505  1.00  0.00
ATOM   2778  N   THR B 337      60.139  23.423  46.095  1.00  0.00
ATOM   2779  CA  THR B 337      58.765  23.151  45.661  1.00  0.00

but not when I have only one chain in the .trr like in this example
(part of .pdb file).

ATOM   2776  O1  PHE   336      41.051  55.857  23.785  1.00  0.00
ATOM   2777  O2  PHE   336      42.809  56.115  22.532  1.00  0.00

VMD can unfortunately not do what I need so is there no way to get the
chain   identifier like in the first example?  

Best regards, Una

Una Bjarnadottir wrote:
> Dear Users, 
> I'm converting trajectory files into .pdb files and when there is only
> the protein chain in them i.e. only the protein but not ligand or
> it does not set any chain identifier to the output .pdb files. But
when there
> is a ligand and inhibitor in them the output will have chains A-B-C.
> I tried whatif to add the chain identifier but it can't read the big
overall file.
> The chain identifier is necessary in some graphics programs so I really
> need this.
> Hope you can help, it will be highly appreciated.

gromacs discards chain identifiers from PDB files when it reads them 
with pdb2gmx and will not re-create them.

Probably free software like VMD http://www.ks.uiuc.edu/Research/vmd/ can 
do what you need without these chain problems, rather than the graphics 
program you're planning to use.

I appreciate that English may not be your first language, but please do 
consider proof-reading your posts and/or using a spell-checker before 
you send. People on this list are much more likely to help you if you 
make it easy for them to do so, rather than work at trying to piece 
together your problem.


More information about the gromacs.org_gmx-users mailing list