[gmx-users] grompp warning: "Overriding Proper Dih. parameters" with type 9 dih.

[Mark Abraham]

Hi,

Ok that makes sense. Otherwise it would have seemed like it had to be a
code bug.

Maybe we could add a warning for including the same file twice? Does
anybody do that deliberately E.g with different preprocessor variables
defined?

Mark

On Tue, 15 Nov 2016 00:30 Elton Carvalho <eltonfc at gmail.com> wrote:

> My apologies,
>
> After careful inspection, I noticed that I had #included a copy of
> this ddt.prm file in charmm36-jun2015.ff/forcefield.itp , so the [
> dihedraltypes ] directive is actually loaded twice, hence the
> warnings. Removing the #include from forcefield.itp and keeping it in
> the .top file eliminated the warnings and the resulting dynamics seems
> sane (read: did not explode).
>
> Lesson learned: don't change the standard forcefield definition files
> when doing preliminary testing. Especially in the end of a 12h layover
> between flights.
>
> Thank you for your attention,
> --
> Elton
>
> On Mon, Nov 14, 2016 at 8:04 PM, Elton Carvalho <eltonfc at gmail.com> wrote:
> > Hello, fellow Gromacs Users,
> >
> > I'm trying to model P3DDT with CGenFF according to the instructions at
> > paramchem.org, running the cgenff_charmm2gmx.py script as provided in
> > their website. All this is being done on gromacs 2016.
> >
> > The script converts the .str file generated by paramchem.org to
> > gromacs syntax and units. As a first test, I ran a signle
> > dodecylthiophene molecule through the process and obtained apparently
> > sane .top and .itp files. The .itp file #includes a .prm file, that
> > contains the parameters fitted by the paramchem software.
> >
> > When running gmx grompp (version 2016), I get these two warnings:
> >
> > === GROMPP WARNING BEGIN ===
> >
> > WARNING 1 [file ddt.prm, line 17]:
> >   Overriding Proper Dih. parameters.
> >   Use dihedraltype 9 to allow several multiplicity terms. Only
> consecutive
> >   lines are combined. Non-consective lines overwrite each other.
> >
> >   old:                                          0 0.8368 1 0 0.8368 1
> >   new: CG2R51   CG2R51    CG321    CG321     9     0.000000
>  1.129680     2
> >
> >
> > WARNING 2 [file ddt.prm, line 18]:
> >   Overriding Proper Dih. parameters.
> >   Use dihedraltype 9 to allow several multiplicity terms. Only
> consecutive
> >   lines are combined. Non-consective lines overwrite each other.
> >
> >   old:                                          0 1.12968 2 0 1.12968 2
> >   new: CG2R51   CG2R51    CG321    CG321     9     0.000000
>  0.000000     3
> >
> > === GROMPP WARNING END ===
> >
> > But the dihedral mentioned is using dihedraltype 9, in lines 16, 17
> > and 18 of the reffered file, as follows:
> >
> > === ddt.prm RELEVANT SECTION BEGIN (lines 10-21)===
> >
> > [ dihedraltypes ]
> > ;      i        j        k        l  func         phi0         kphi  mult
> >   CG2R51   CG2R51   CG2R51    CG321     9   180.000000    16.736000     2
> >    CG321   CG2R51   CG2R51   SG2R50     9   180.000000    29.288000     2
> >    CG321   CG2R51   CG2R51    HGR51     9   180.000000     4.184000     2
> >   CG2R51   CG2R51    CG321    CG321     9     0.000000     0.836800     1
> >   CG2R51   CG2R51    CG321    CG321     9     0.000000     1.129680     2
> >   CG2R51   CG2R51    CG321    CG321     9     0.000000     0.000000     3
> >   CG2R51    CG321    CG321    CG321     9     0.000000     0.167360     3
> >   CG2R51    CG321    CG321     HGA2     9     0.000000     0.836800     3
> >
> > === ddt.prm RELEVANT SECTION END ===
> >
> > As you can see, the dihedraltype is 9 and the different multiplicities
> > of the "CG2R51   CG2R51    CG321    CG321" dihedral are on adjacent
> > lines (16, 17 and 18 of the original file. Note that the first warning
> > is about overriding the parameters on line 16 with those on line 17,
> > so this dihedral is not defined somewhere else).  No wildcard dihedral
> > parameters are present in the loaded .itp files.
> >
> > Why does grompp warn me that it's "Overriding Proper Dih. parameters",
> > even though the parameters are entered (to the best of my knowledge)
> > as instructed both in the warning and in Section 5.3.3 of the
> > Reference Manual? How can I check whether it really did override the
> > parameter or added the different terms?
> >
> > Thanks in advance,
> > --
> > Elton Carvalho
>
>
>
> --
> Elton Carvalho
> --
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