[gmx-developers] RTP and RES block names

[Berk Hess]

On 02/12/2013 09:05 PM, Mark Abraham wrote:
>
>
> On Tue, Feb 12, 2013 at 1:48 PM, Anton Feenstra <k.a.feenstra at vu.nl 
> <mailto:k.a.feenstra at vu.nl>> wrote:
>
>     On 12/02/13 12:03, Alexey Shvetsov wrote:
>
>         ? ?????? ?? 12 ??????? 2013 11:26:30 ???????????? Anton
>         Feenstra ???????:
>
>             On 11/02/13 17:44, Alexey Shvetsov wrote:
>
>                 Hi all!
>
>                 Is there a reson why resnames and rtp block names
>                 arent case sensetive?
>                 Actualy I plan to add glycam06.ff port to gromacs. It
>                 has about ~1300 rtp
>                 blocks that are case sensetive.
>
>
>             It's error prone, that is the (main) reason they are case
>             insensitive in
>             Gromacs. Moreover, in the PDB, anything is (or at least
>             used to be)
>             stored in upper case anyway, so there didn't seem to be
>             any sense in
>             having lower case (or case sensitive) residue names.
>
>
>         Thats true for amino and nucleic acids, but in case for sugars
>         building block
>         and glycam resname convention it doesnt work. Also pdb file
>         format doesnt
>         states that resname should be case insensetive.
>
>
>             Perhaps adding a keyword/switch option in the particular
>             (rtp/res)
>             file could enable case sensitive matching on a per file basis?
>
>
>         May be better to enable case sensetive resnames by default? As
>         it was done
>         before for atomnames?
>
>
>     Sounds like a good suggestion to me (I didn't
>     know that atomnames were already case sensitive).
>
>
> I can't think of a good reason why not. But I can't think of someone 
> with the time to do it, either :-)
>
> Mark
>
The original reason was that the rtp entry names exactly matched residue 
names,
the case of which is not unique. So simply making it case sensitive will 
be problematic.
One option could be to first search case sensitive and if no rtp entry 
is found for a residue (name)
search case insensitive.

Cheers,

Berk


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