[gmx-users] Re: Re: trjconv and missing chain identifier
tsjerkw at gmail.com
Mon Mar 5 11:19:27 CET 2007
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
Hope it helps,
On 3/5/07, Una Bjarnadottir <una.bjarnadottir at ucd.ie> wrote:
> 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.
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
3584 CH Utrecht
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