[gmx-users] norleucine topology

[Marc Bruning]

i used the amberGS ff from the amber gromacs ports. hdb and rtp entries are 
attached.

On Sunday 20 August 2006 13:38, David van der Spoel wrote:
> merc mertens wrote:
> > dear list,
> >
> > to get a topology for norleucine i combined parameters from LEU (N,CA,CB,
> > plus H´s, C, O) and MET (CG, CE, plus H´s). to get CD and its H´s i took
> > parameters from MET CG as well. finally i adjusted the charges of CG and
> > CD to get a residue topology with zero charge. can it be that easy???
> >
> > merc
>
> in this case, yes. which ff did you use?
> can you contribute the rtp and hdb entries?
-------------- next part --------------
[ NLE ]
 [ atoms ]
     N    amber94_34  -0.41570     1
     H    amber94_17   0.27190     2
    CA    amber94_11  -0.05180     3
    HA    amber94_19   0.09220     4
    CB    amber94_11  -0.11020     5
   HB1    amber94_18   0.04570     6
   HB2    amber94_18   0.04570     7
    CG    amber94_11  -0.11020     8
   HG1    amber94_19   0.04400     9
   HG2    amber94_19   0.04400    10
    CD    amber94_11  -0.12460    11
   HD1    amber94_19   0.04400     9
   HD2    amber94_19   0.04400    10
    CE    amber94_11  -0.05360    12
   HE1    amber94_19   0.06840    13
   HE2    amber94_19   0.06840    14
   HE3    amber94_19   0.06840    15
     C    amber94_2    0.59730    16
     O    amber94_41  -0.56790    17
 [ bonds ]
     N     H
     N    CA
    CA    HA
    CA    CB
    CA     C
    CB   HB1
    CB   HB2
    CB    CG
    CG   HG1
    CG   HG2
    CG    CD
    CD   HD1
    CD   HD2
    CD    CE
    CE   HE1
    CE   HE2
    CE   HE3
     C     O
    -C     N
 [ dihedrals ]
    CA     C    +N    +H    backbone_prop_1
     O     C    +N    +H    backbone_prop_2
    -C     N    CA    CB    backbone_prop_3
    -C     N    CA     C    backbone_prop_4
    CA     C    +N   +CA    backbone_prop_1
     O     C    +N   +CA    backbone_prop_1
 [ impropers ]
    -C    CA     N     H
    CA    +N     C     O

-------------- next part --------------
NLE     6
1       1       H       N       -C      CA      
1       5       HA      CA      N       CB      C       
2       6       HB      CB      CA      CG      
2       6       HG      CG      CB      CD      
2       6       HD      CD      CG      CB      
3       4       HE      CE      CD      CG