I am trying to figure out changes made in v 4.5.1 in share/gromacs/top.
In earlier versions, there were some defined variables, e.g., hyp_prop_1
for hydroxyprolines and <br><br>grep -r hyp_prop_1 ~/gromacs_4.0.5/share/gromacs/<div id=":ia">top/<br>
<br>would show ~15 lines, including for example:<br><br>ffamber99bon.itp:#define
hyp_prop_1 0.65270 1.95811 12.46832 -2.61082
0.00000 0.00000 ; HYP for amber99: S Park, R J Radmer, T E Klein
& V S Pande (submitted).<br>
<br>If I grep the version 4.5.1 directories, nothing is found. Grepping
either for hyp or for 1.95811 (one of the values above) does not find
anything either. Seaarching for one of the author names from the above
output finds entries in aminoacids.rtp files, but there are no dihedral
parameters for Hyp listed there. Where are the Hyp torsion parameters ?<br>
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