[gmx-developers] Case sensetive Moleculetypes

Berk Hess hess at kth.se
Wed Nov 25 14:33:29 CET 2015

On 11/25/2015 01:55 PM, Alexey Shvetsov wrote:
> David van der Spoel писал 25-11-2015 14:58:
>> On 25/11/15 12:36, Alexey Shvetsov wrote:
>>> Hi!
>>> Is it intentional to have case insensetive moleculetypes?
>>> Use case where case sensetive types needed is for example system 
>>> created
>>> from pdb file that has more then 23+ chains. PDB format allows to use
>>> both uppercase and lowercase letters for chain names. So if you for
>>> example has protein chain 'a' and protein chain 'A' then grompp will
>>> fail with error about redefinition of molecule type. Patch uploaded to
>>> gerrit.
>>> [0] https://gerrit.gromacs.org/5384
>> It is intentional but whether it is a good idea is another matter. It
>> would be irritating to have grompp fail because of writing sol instead
>> of SOL. One could first check for strcmp and if one doesn't find sol
>> try SOL and give a warning.
> Ok. lets try the way you suggested.
This won't work. That way you will always find the first molecule type 
in the list.
You should check all case insensitive matches. If there is only one, use 
that. If there is more than one, pick the one where the case mathes (and 
fatal error if there is no exact match).

>> -- 
>> David van der Spoel, Ph.D., Professor of Biology
>> Dept. of Cell & Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone:    +46184714205.
>> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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