[gmx-users] Two [ dihedrals ] sections in topology

[Lara Bunte]

Hi

After pdb2gmx I have two [ dihedrals ] sections in my topology. The first block is empty, the second block is correct with my parameters. 


An an example: 


First block:
[ dihedrals ]
;  ai    aj    ak    al funct            c0            c1            c2            c3            c4            c5
    2     1    19     8     5
    6     8     9    10     5


Second block:
[ dihedrals ]
;  ai    aj    ak    al funct            c0            c1            c2            c3
    1     8     6     4     5    180   100
    1     2     4     5     5    180   100


What could be the reason for this? What do I have to change in my force field folder (CHARMM27) to fix this?

In my .rtp file in the force field folder I have only this section for dihedrals

[ impropers ]
O4     N1      C2       N3     180   100
N1     C2      N3       H3     180   100


I declared my [ bondedtypes ] as the following:

[ bondedtypes ]
; bonds  angles  dihedrals  impropers
     1       1          5          5


Thanks for help
Greetings