[gmx-developers] Nomenclature Inconsistency between *nb.itp and *.rtp in ffG53a5 and ffG53a6 (CH2r vs CH2R)

[Justin A. Lemkul]

Diana Lousa wrote:
> Hello,
> 
> I noticed that there is an inconsistency between the files ffG53a6nb.itp 
> and ffG53a6.rtp, and between the corresponding files in the ffG53a5 . 
> The atom type that is used for some CH2 atoms inside rings (e.g. CB CG 
> CD in Proline) is defined as CH2r type in the fG53a6nb.itp file :
> 
> CH2r    6     0.000      0.000     A  0.0073342096  2.8058209e-05
> 
> However, it is defined as CH2R in the ffG53a6.rtp file, in the residues 
> that contain this type of atom. As an example,  for Proline, the 
> definitions are:
> 
> [ PRO ]
>  [ atoms ]
>     N     N     0.00000     0
>    CA   CH1     0.00000     1
>    CB  CH2R     0.00000     1
>    CG  CH2R     0.00000     2
>    CD  CH2R     0.00000     2
>     C     C       0.450     3
>     O     O      -0.450     3
> 
> Is GROMACS case insensitive? Can I run simulations, using ffG53a6, 
> without worrying about this?
> 

It would seem so.  I've run several simulations of proline-containing proteins 
under G53a6.  None of them have ever had an error.

-Justin

> 
> Thanks in advance.
> 
> 
> 
> -- 
> Diana Lousa
> PhD student
> Protein Modelling Laboratory
> ITQB/UNL
> Oeiras, Portugal
> 
> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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