[gmx-developers] Atom names in GMX

[Justin Lemkul]

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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>>>>>
>>>>> --
>>>>> 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
>>
>> ==================================================
>

-- 
==================================================

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

==================================================