[gmx-developers] RTP and RES block names
alexxy at omrb.pnpi.spb.ru
Tue Feb 12 21:13:25 CET 2013
В письме от 12 февраля 2013 21:05:33 пользователь Mark Abraham написал:
> On Tue, Feb 12, 2013 at 1:48 PM, Anton Feenstra <k.a.feenstra at vu.nl> wrote:
> > On 12/02/13 12:03, Alexey Shvetsov wrote:
> >> В письме от 12 февраля 2013 11:26:30 пользователь Anton Feenstra написал:
> >>> 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 :-)
Ok. If there not too many objections I'll post patch that will do it tommorow
to gerrit. Seems like its only few lines changes in 4 files =)
Alexey 'Alexxy' Shvetsov
Petersburg Nuclear Physics Institute, NRC Kurchatov Institute,
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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