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

Alexey Shvetsov alexxyum at gmail.com
Thu Mar 11 12:32:02 CET 2010

I have script to rename residues to use with amber ff. So if anyone
intresting in it i can share it.

PS btw will amber ff included in gromacs 4.1?
PPS also seem renaming can be done via pdb2gmx with simple patch

2010/3/11 Erik Marklund <erikm at xray.bmc.uu.se>:
> 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
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> Erik Marklund, PhD student
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Best Regards,
Alexey 'Alexxy' Shvetsov
Petersburg Nuclear Physics Institute, Russia
Department of Molecular and Radiation Biophysics
Gentoo Team Ru
Gentoo Linux Dev
mailto:alexxyum at gmail.com
mailto:alexxy at gentoo.org
mailto:alexxy at omrb.pnpi.spb.ru

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