<div>Dear gmx-users,</div><div><br></div><div>Does anyone know where can I find any explanations about the atom names in ffbonded.itp file in oplsaa.ff? I am trying to compare the amino acids' parameters in gromacs 4.5.4 with in tinker. Or where to find the default parameters gromacs takes for amino acids in its aminoacids.rtp file?</div>
<div><br></div><div>For example, it is hard to guess what are C*, C_2 and C= in ffbonded.itp file:</div><div><br></div><div> C* HC 1 0.10800 284512.0 ;</div><div> C C3 1 0.15220 265265.6 ; END</div>
<div> C_2 C3 1 0.15220 265265.6 ; END</div><div>...</div><div><div>C= C= HC 1 120.000 292.880 ; wlj</div><div> C C= HC 1 119.700 292.880 ;</div></div><div><br></div>
<div>Thanks!</div><div><br></div><div>jia</div>