[gmx-developers] Atom names in GMX

David van der Spoel spoel at xray.bmc.uu.se
Thu May 7 12:55:36 CEST 2015 

On 2015-05-07 12:34, Alexey Shvetsov wrote:
> Hi!
>
> So in principle for rtp block names it will be good to have some setting
> in for exampl ffname.ff/forcefield.itp
>
No, because this is not read when processing the rtp file.

> like
>
> [ defaults ]
> ; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
> case-sensetive-rtp
> 1               2               yes             0.5     0.8333   yes|no
>
> Also are there some already ongoin work on e.g per molecule or per rtp
> block fudgeQQ and fudgeLJ?
>
>
> Berk Hess писал 07-05-2015 08:55:
>> 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
>>>>>>>>>>>> -- 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
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> 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
>>>>>>>
>>>>>>> ==================================================
>>>>>>
>>>>>
>>>
>


-- 
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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