[gmx-developers] Atom names in GMX
Alexey Shvetsov
alexxy at omrb.pnpi.spb.ru
Thu May 7 12:34:24 CEST 2015
Hi!
So in principle for rtp block names it will be good to have some setting
in for exampl ffname.ff/forcefield.itp
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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>>>>>>>>>>
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>>>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers
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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:
>>>>>>>> ------
>>>>>>>> [1]
>>>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List
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>>>>>>>> [3]
>>>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers
>>>>>>>
>>>>>>
>>>>>> -- ==================================================
>>>>>>
>>>>>> 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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