[gmx-developers] Atom names in GMX

[Alexey Shvetsov]

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 :\

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
> 
> ==================================================

-- 
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