<div>Dear Gromacs Users</div>
<div> </div>
<div>I am confused about definition of improper dihedral angle in charmm27, which is compared to oplsaa.</div>
<div> </div>
<div>Why charmm ff in gromacs give <strong>double</strong> items for the same dihedral angle.</div>
<div>e.g. for charmm27 ASN</div>
<div> CG ND2 CB OD1<br> <font color="#ff0000"> CG CB ND2 OD1<br></font> ND2 CG HD21 HD22<br> <font color="#ff0000">ND2 CG HD22 HD21<br></font><font style="BACKGROUND-COLOR:#ffffff" color="#000000">in opls aa for ASN</font></div>
<div> CG CB CA C dih_ASN_chi1_C_C_C_CO<br> CA CB CG ND2 dih_ASN_chi2_C_C_CO_N<br></div>
<div>Thanks for advance!</div>
<div> </div>
<div>Tom</div>
<div> </div>
<div>PS:</div>
<div> </div>
<div>the detail is as follows </div>
<div> </div>
<div>------------------------------------------------</div>
<div><strong>in charmm27.ff/aminoacids.rtp</strong></div>
<div>[ ASN ]<br> [ atoms ]<br> N NH1 -0.47 0<br> HN H 0.31 1<br> CA CT1 0.07 2<br> HA HB 0.09 3<br> CB CT2 -0.18 4<br> HB1 HA 0.09 5<br>
HB2 HA 0.09 6<br> CG CC 0.55 7<br> OD1 O -0.55 8<br> ND2 NH2 -0.62 9<br> HD21 H 0.32 10<br> HD22 H 0.30 11<br>
C C 0.51 12<br> O O -0.51 13<br> [ bonds ]<br> CB CA<br> CG CB<br> ND2 CG<br> N HN<br> N CA<br> C CA<br>
C +N<br> CA HA<br> CB HB1<br> CB HB2<br> ND2 HD21<br> ND2 HD22<br> C O<br> CG OD1<br> [ impropers ]<br> N -C CA HN<br>
C CA +N O<br><font color="#ff0000"> CG ND2 CB OD1<br> CG CB ND2 OD1<br> ND2 CG HD21 HD22<br> ND2 CG HD22 HD21<br></font> [ cmap ]<br>
-C N CA C +N</div>
<div>-------------------------------------------</div>
<div>in<strong> oplsaa.ff/aminoacids.rtp</strong></div>
<div>[ ASN ]<br> [ atoms ]<br> N opls_238 -0.500 0<br> H opls_241 0.300 0<br> CA opls_224B 0.140 1<br> HA opls_140 0.060 1<br> CB opls_136 -0.120 2<br> HB1 opls_140 0.060 2<br>
HB2 opls_140 0.060 2<br> CG opls_235 0.500 3<br> OD1 opls_236 -0.500 3<br> ND2 opls_237 -0.760 4<br> HD21 opls_240 0.380 4<br> HD22 opls_240 0.380 4<br>
C opls_235 0.500 5<br> O opls_236 -0.500 5<br> [ bonds ]<br> N H<br> N CA<br> CA HA<br> CA CB<br> CA C<br> CB HB1<br> CB HB2<br> CB CG<br> CG OD1<br>
CG ND2<br> ND2 HD21<br> ND2 HD22<br> C O<br> -C N<br> [ dihedrals ] ; override some with residue-specific ones<br> N CA CB CG dih_ASN_chi1_N_C_C_C<br> CG CB CA C dih_ASN_chi1_C_C_C_CO<br>
CA CB CG ND2 dih_ASN_chi2_C_C_CO_N<br></div>