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

Lara Bunte lara.bunte at yahoo.de
Thu May 17 17:16:38 CEST 2012


Just for correct understanding: In this "empty" [ dihedrals ] bock are 11 lines without equilibrium angle and force constant, that looks like:

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

Did this mean, that this are really physical dihedrals, that were given by pdb2gmx and the only reason that they are "empty" is, that they are not parametrized? 
Is this correct?


----- Ursprüngliche Message -----
Von: Justin A. Lemkul <jalemkul at vt.edu>
An: Lara Bunte <lara.bunte at yahoo.de>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Gesendet: 17:02 Donnerstag, 17.Mai 2012
Betreff: Re: [gmx-users] Two [ dihedrals ] sections in topology

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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