[gmx-users] Two [ dihedrals ] sections in topology
francesco.oteri at gmail.com
Thu May 17 17:58:37 CEST 2012
2012/5/17 Lara Bunte <lara.bunte at yahoo.de>
> 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
> Is this correct?
No, it means that defaukt values (i.e. listed in [ dihedraltypes ] section
) will be applied
> ----- 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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Cordiali saluti, Dr.Oteri Francesco
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