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

[Justin A. Lemkul]

On 5/17/12 10:48 AM, Lara Bunte wrote:
> Hi
>
> grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
>
> gives me errors like
>
> ERROR 1 [file topol.top, line 233]:
>    No default Improper Dih. types
>
> and so on. This line 233 is the starting of my empty [ dihedrals ] block. I erase it by hand out of my topology, so that only the correct [ dihedrals ] out of the .rtp and ffbonded.itp file are in the topology. After this grompp works without error and even without any warning.
>
>
> So the question how to force pdb2gmx to use only my [ dihedrals ] block is important for me, because I don't like to erase it always by hand out of the topol.top file.
>

This goes back to something that has been stated several times now, and was 
discussed the other day.  If pdb2gmx finds 4 atoms connected via bonds, it 
assigns a dihedral to it.  That's just physically real.  If your force field 
then doesn't have parameters for that particular interaction, you get the error 
shown above.  That doesn't mean you should go deleting things until grompp 
"works" because what will result will likely be senseless.

If your "empty" (which is not really empty, as we've been saying) dihedrals are 
causing the problems, then you need to add parameters for them in ffbonded.itp 
or in the topology itself, not hack the topology apart.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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