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

[Elton Carvalho]

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