<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
On 11/02/2012 9:54 AM, Tom wrote:
<blockquote
cite="mid:CAARYzz51xFeeuGz-wEuH8o00SU1gVTcOSx2JW-cPBZpcUj_UpA@mail.gmail.com"
type="cite">
<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></div>
</blockquote>
<br>
These are not duplicates. Atom ordering is significant. These
*improper* dihedral angles are enforcing planarity of the amide
moiety. This is done by influencing dihedral angles along intra-atom
vectors where there is no bond. OPLS/AA is working differently
somehow.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAARYzz51xFeeuGz-wEuH8o00SU1gVTcOSx2JW-cPBZpcUj_UpA@mail.gmail.com"
type="cite">
<div><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>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
</blockquote>
<br>
</body>
</html>