[gmx-developers] Atom names in GMX

Berk Hess hess at kth.se
Thu May 7 07:46:34 CEST 2015 

Hi,

I see now that glycam uses bond-atom types (whereas Amber doesn't). The 
case sensitivity for normal atom types was needed for Charmm and it 
works there. I would think that also for consistency it's better to have 
bond-atom types case sensitive.

But making rtp building block names case sensitive is problematic. Atom 
types are only used internally in a force field, so the force field only 
needs to be internally consistent. Block usually need to be matched 
against residue names and we can't assume that input like pdb files 
always using consistent case. The only solution here is (apart from 
renaming rtp block names), is to internally use case sensitivity and 
have the resname-rtp matching case insensitive by default, but 
optionally case sensitive.

Cheer,

Berk

On 05/07/2015 12:14 AM, Alexey Shvetsov wrote:
> 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
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>>>>>>>>>
>>>>>>>>
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>>>>>>>> [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
>>>>>>>
>>>>>>>
>>>>>>> Links:
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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
>>>>>
>>>>> ==================================================
>>>>
>>>
>

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