Hello,<br><br>I noticed that there is an inconsistency between the
files ffG53a6nb.itp and ffG53a6.rtp, and between the corresponding
files in the ffG53a5 . <br>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 :<br clear="all">
<br>CH2r 6 0.000 0.000 A 0.0073342096 2.8058209e-05<br><br>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:<br>
<br>[ PRO ]<br> [ atoms ]<br> N N 0.00000 0<br> CA CH1 0.00000 1<br> CB CH2R 0.00000 1<br> CG CH2R 0.00000 2<br> CD CH2R 0.00000 2<br> C C 0.450 3<br>
O O -0.450 3<br><br>Is GROMACS case insensitive? Can I run simulations, using ffG53a6, without worrying about this?<br><br><br>Thanks in advance.<br><font color="#888888"><font color="#888888"><br></font></font><br clear="all">
<br>-- <br>Diana Lousa<br>PhD student<br>Protein Modelling Laboratory<br>ITQB/UNL<br>Oeiras, Portugal<br>