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

[Mark Abraham]

On 15/05/2012 8:47 PM, Lara Bunte wrote:
> 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?

Two blocks of dihedrals are normal output for pdb2gmx - one for proper 
and one for improper dihedrals.

>
> 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

This produces your second block of type 5 dihedrals, given what you have 
said below.

>
>
> I declared my [ bondedtypes ] as the following:
>
> [ bondedtypes ]
> ; bonds  angles  dihedrals  impropers
>       1       1          5          5

Those are angle, dihedral and improper function types that are abnormal 
for CHARMM27. Using these in your .rtp means that you are no longer 
using CHARMM27. It might be reasonable for you to do this, but you need 
to be absolutely sure why. Importing a topology from another force field 
is not an acceptable reason.

Mark