[gmx-developers] 4-letter residue codes in PDB files

Erik Marklund erikm at xray.bmc.uu.se
Thu Mar 11 09:31:43 CET 2010

Mark Abraham skrev:
> On 11/03/2010 10:25 AM, Justin MacCallum wrote:
>>> Unless PDB with 4-letter residue names is required for some external
>>> program, choosing to write .gro files would circumvent the problem. 
>>> This
>>> approach should be preferred where possible, rather than add to the
>>> chaos of standards-incompatible pseudo-PDB-format there is out there.
>>> Mark
>> This is indeed the case. I'm working with external programs that 
>> require PDB files. As it stands, if I take a pdb file and run it 
>> through gromacs and my external utility, I then have to edit the file 
>> before gromacs will accept it again. Ideally gromacs should be 
>> willing to eat its own output.
> Sure. Sometimes the unix head, tail, cut and paste tools can do the 
> job. Send the header and footer to files so named, grep out the middle 
> lines, chop the middle into columns 1-x and x-80. Now paste a 
> corrected columns 1-x that you prepared earlier to the appropriate 
> positions in x-80. Then concatenate that to the header and footer and 
> you're done.
> sed or perl solutions are also possible, and necessary if you have 
> pseudo-trajectories in your PDB files.
> Mark
Indeed. I think sed is your best friend here. sed 's/NTH /NTHR/' or 
something along those lines.


Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/

More information about the gromacs.org_gmx-developers mailing list