[gmx-developers] preserving residue numbers

[Roland Schulz]

Hi,

one limitation is that currently both the residue number and the charge
group number have to be consecutive in the topology file. Thus if you have a
charge group that spans two residues, you need to reorder the atoms, so
that the atoms which are part of the spanning group are at the end/beginning
of the residue. And if you have a branched molecule - so that one residue
can have three spanning charge groups - it does not work. We ended up having
to set the residue number to 1 for the whole molecule.

Is this limitation, that residue and charge group have to be consecutive in
the topology, necessary?

Roland

On Tue, Mar 3, 2009 at 10:14 AM, Anton Feenstra <feenstra at few.vu.nl> wrote:

> Berk Hess wrote:
>
>> Hi,
>>
>> The past years we received a lot of requests for Gromacs to preserve the
>> residue numbering of the original pdb file.
>> Currently Gromacs simply renumbers all residues consecutively starting
>> from one.
>> I have now implemented free residue numbering (but not committed yet),
>> including pdb insertion codes.
>> This allows for more freedom, but therefore also some choices nedd to be
>> made.
>>
>> A limitation of Gromacs, which I think we would like to preserve, is that
>> residue numbers are stored
>> per molecule type and therefore one can not have a different numbering in
>> different molecules
>> of the same type.
>>
>
> Agreed. This should cover most cases anyway.
>
>  My current implementation preserves the residue numbers for
>> multiple-residue molecules,
>> but for single residue molecules (for instance water and ions) the
>> residues will continue
>> numbering from the last residue in the last molecule before.
>> For a protein in water this gives the most desirable behavior. Although
>> even here there are small
>> issues. For instance the choice of pdb2gmx writing a gro file with the
>> original pdb res numbers
>> (e.g. for 2lzm the last prot. resnr is 164, but the first water is 166),
>> which is then not what Gromacs
>> will produce later, because the tpr made from the top file will number the
>> waters starting at 165.
>> Should the pdb2gmx output keep the pdb resnrs for the water or use the
>> Gromacs convention?
>>
>
> I'd say output of pdb2gmx could retain pdb numbering as close as possible,
> even though subsequent processing might lead to more extensive residue
> renumbering.
>
>  Another effect is that for for instance polymers there will be many
>> residues with resnr 1 in the system.
>> This is very convenient if you want to select all end groups, but less
>> convenient if you want to select
>> a particular residue, although this can be done by selecting chains or
>> molecules.
>>
>> Finally several analysis tools write values as a function of residue
>> number.
>> For a single protein it might be very convenient to have the original
>> residue numbers in the output.
>> But if you have 4 chains, all with resnrs 1 to 200, things get messy.
>>
>> Do you have comments or suggestions?
>>
>
> Perhaps some options could control pdb2gmx behaviour here? Like in your
> 4-chain example you might want the options to preserve, or number
> continuously, or add an offset, so chains start at 1, 1001, 2001, 3001?
>
> Also, adding a 'renumber residues' option to an existing tool (editconf?)
> might be convenient, to create numbering schemes for different (display)
> purposes. I vaguely remember seeing such option somewhere, but could not
> locate it just now.
>
> --
> Groetjes,
>
> Anton
>  _____________ _______________________________________________________
> |             |                                                       |
> |  _   _  ___,| K. Anton Feenstra                                     |
> | / \ / \'| | | IBIVU/Bioinformatics - Free University  Amsterdam     |
> |(   |   )| | | De Boelelaan 1083A - 1081 HV Amsterdam - Netherlands  |
> | \_/ \_/ | | | Tel +31 20 59 87783 - Fax +31 20 59 87653 - Room P136 |
> |             | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/<http://www.few.vu.nl/%7Efeenstra/>        |
> |             | "You Could Be a Shadow" (The Breeders)                |
> |_____________|_______________________________________________________|-
> Show quoted text -
>
> _______________________________________________
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-developers-request at gromacs.org.
>



-- 
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20090303/3bdf3e51/attachment.html>