[gmx-developers] Atom names in GMX
Alexey Shvetsov
alexxy at omrb.pnpi.spb.ru
Thu May 7 00:14:14 CEST 2015
Hi Berk!
This change solves problem for me https://gerrit.gromacs.org/4552
So now atomtypes are realy case sensetive
Are there possible caveates to make rtp block names case sensetive?
Berk Hess писал 07-05-2015 00:32:
> 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
>>>>>>>>> -- Gromacs Developers mailing list
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>>>>>>>
>>>>>>> -- 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
>>>>
>>>> ==================================================
>>>
>>
--
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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