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

[Tsjerk Wassenaar]

Hi Una,

You can do it in pymol (http://pymol.sourceforge.org/):

alter i. x-y, chain="Z"

where x is the first residue number and y the last of the chain you
want to give an identifier, and Z is the one-letter chain id.

You can afterwards write the .pdb file again, with the chain ids, but
you have to note that under normal circumstances pymol rearranges the
atom order in residues (which you can overrule using 'set
retain_order, on')

Hope it helps,

Tsjerk

On 3/5/07, Una Bjarnadottir <una.bjarnadottir at ucd.ie> wrote:
> Mark
>
> 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
> inhibitor
> > 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.
>
> Mark
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623