[gmx-developers] Atom names in GMX

[Berk Hess]

Hi,

I made atom types case sensitive in 2010:

in gpp_atomtype.c
int get_atomtype_type(const char *str, gpp_atomtype_t ga)
{
     int i;

     /* Atom types are always case sensitive */
     for (i = 0; (i < ga->nr); i++)
     {
         if (strcmp(str, *(ga->atomname[i])) == 0)
         {
             return i;
         }
     }

     return NOTSET;
}

But that doesn't seem to work here then?

Cheers,

Berk

On 05/06/2015 11:14 PM, Justin Lemkul wrote:
>
>
> On 5/6/15 5:11 PM, Alexey Shvetsov wrote:
>> Hi Justin!
>>
>> Well Os cames from original glycam forcefield, they use it only for 
>> sugars (so
>> OS atomtype still will be used in protein). Same came for resnames :\
>>
>
> Most everything in GROMACS is case-insensitive; the more I think about 
> it, probably case sensitivity wasn't removed, it more likely never 
> existed.
>
> -Justin
>
>> Justin Lemkul писал 07-05-2015 00:06:
>>> On 5/6/15 5:02 PM, Alexey Shvetsov wrote:
>>>> Mark Abraham писал 06-05-2015 23:56:
>>>>> Hi,
>>>>>
>>>>> OK that could well be right :-( Looks like a job for sed, then! (for
>>>>> now)
>>>>
>>>> Or making them case sensetive (if current behavior wasnt done for 
>>>> some purpose)
>>>>
>>>
>>> IIRC, case-sensitivity was specifically removed.  It has caused some
>>> consternation on the user list before, with regards to this exact
>>> issue.  FWIW, this is definitely the case with atom *types* but I am
>>> not sure about atom *names* - the latter seems less significant.
>>>
>>> In general, I am of the opinion that if you are relying on case
>>> sensitivity for proper function, that's just asking for trouble.  Why
>>> OS and Os when OS and OS2 unambiguously perform the same function?
>>> That's a general debate, and ultimately up to the force field
>>> designers.  I'm used to up to 6 characters for CHARMM - the naming is
>>> designed to make the chemical nature of the atom obvious :)
>>>
>>> -Justin
>>>
>>>>>
>>>>> Mark
>>>>>
>>>>> On Wed, May 6, 2015 at 10:53 PM Alexey Shvetsov
>>>>> <alexxy at omrb.pnpi.spb.ru> wrote:
>>>>>
>>>>>> Hi!
>>>>>>
>>>>>> Mark Abraham писал 06-05-2015 23:28:
>>>>>>> Hi,
>>>>>>>
>>>>>>> Some things might be, I seem to recall. But there's lots of
>>>>>> different
>>>>>>> kinds of fields, so best would be to try it out. If it can't be
>>>>>>> matched...
>>>>>>
>>>>>> It seems to be case insensetive = As well as for rtp block names.
>>>>>>
>>>>>> From amber99sb+glycam additions (whic mostly uses atom names like
>>>>>> this
>>>>>> Os Oh etc)
>>>>>>
>>>>>> C OS 1 0.1323 376560.0 ; new99
>>>>>> C Os 1 0.1323 376812 ; Parm99
>>>>>>
>>>>>> grompp thinks that there are redefined params
>>>>>>
>>>>>> WARNING 1 [file ffbonded.itp, line 120]:
>>>>>> Overriding Bond parameters.
>>>>>>
>>>>>> old: 0.1323 376560
>>>>>> 0.1323
>>>>>> 376560
>>>>>> new: C Os 1 0.1323 376812
>>>>>>
>>>>>> PS same for rtp block names (glycam for example have ~2700 blocks)
>>>>>>
>>>>>>>
>>>>>>> Mark
>>>>>>>
>>>>>>> On Wed, May 6, 2015 at 10:21 PM Alexey Shvetsov
>>>>>>> <alexxy at omrb.pnpi.spb.ru> wrote:
>>>>>>>
>>>>>>>> Hi all!
>>>>>>>>
>>>>>>>> Are atomnames in forcefields case sensetive?
>>>>>>>>
>>>>>>>> -- 
>>>>>>>> Best Regards,
>>>>>>>> Alexey 'Alexxy' Shvetsov, PhD
>>>>>>>> Department of Molecular and Radiation Biophysics
>>>>>>>> FSBI Petersburg Nuclear Physics Institute, NRC Kurchatov
>>>>>> Institute,
>>>>>>>> Leningrad region, Gatchina, Russia
>>>>>>>> mailto:alexxyum at gmail.com
>>>>>>>> mailto:alexxy at omrb.pnpi.spb.ru
>>>>>>>> -- 
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>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers 
>>>>>
>>>>>> [3]
>>>>>>
>>>>>> -- 
>>>>>> Best Regards,
>>>>>> Alexey 'Alexxy' Shvetsov, PhD
>>>>>> Department of Molecular and Radiation Biophysics
>>>>>> FSBI Petersburg Nuclear Physics Institute, NRC Kurchatov Institute,
>>>>>> Leningrad region, Gatchina, Russia
>>>>>> mailto:alexxyum at gmail.com
>>>>>> mailto:alexxy at omrb.pnpi.spb.ru
>>>>>
>>>>>
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>>>>>
>>>>
>>>
>>> -- 
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ==================================================
>>
>