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

Diana Lousa dlousa at itqb.unl.pt
Thu Mar 19 17:47:48 CET 2009


I noticed that there is an inconsistency between the files ffG53a6nb.itp and
ffG53a6.rtp, and between the corresponding files in the ffG53a5 FF.
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  (line 20):

CH2r    6     0.000      0.000     A  0.0073342096  2.8058209e-05

Whereas 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 sensitive?. Can this be a source of errors?

Thanks in advance.

Diana Lousa
PhD student
Protein Modelling Laboratory
Oeiras, Portugal
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